Starting phenix.real_space_refine on Thu Mar 5 14:39:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6whu_21676/03_2026/6whu_21676.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whu_21676/03_2026/6whu_21676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6whu_21676/03_2026/6whu_21676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whu_21676/03_2026/6whu_21676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6whu_21676/03_2026/6whu_21676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whu_21676/03_2026/6whu_21676.map" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.781 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 138 5.16 5 Cl 8 4.86 5 C 14988 2.51 5 N 3780 2.21 5 O 4452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23368 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5804 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 25, 'HIS:plan': 4, 'GLU:plan': 18, 'GLN:plan1': 8, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 280 Chain: "B" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5745 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 28, 'TRANS': 742} Chain breaks: 5 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 12, 'ARG:plan': 11, 'GLN:plan1': 5, 'TYR:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 213 Chain: "C" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5804 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 25, 'HIS:plan': 4, 'GLU:plan': 18, 'GLN:plan1': 8, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 280 Chain: "D" Number of atoms: 5745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5745 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 28, 'TRANS': 742} Chain breaks: 5 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 12, 'ARG:plan': 11, 'GLN:plan1': 5, 'TYR:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 213 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.76, per 1000 atoms: 0.25 Number of scatterers: 23368 At special positions: 0 Unit cell: (141.11, 149.33, 186.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 138 16.00 P 2 15.00 O 4452 8.00 N 3780 7.00 C 14988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.02 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " 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=2.04 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.02 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " 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=2.04 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1002 " - " ASN A 297 " " NAG A1003 " - " ASN A 224 " " NAG B 902 " - " ASN B 74 " " NAG B 905 " - " ASN B 688 " " NAG C1002 " - " ASN C 297 " " NAG C1003 " - " ASN C 224 " " NAG D 902 " - " ASN D 74 " " NAG D 905 " - " ASN D 688 " " NAG E 1 " - " ASN B 542 " " NAG F 1 " - " ASN D 542 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 921.4 milliseconds 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM A1001 " pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5824 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 32 sheets defined 41.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.665A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 143 through 159 removed outlier: 3.843A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 245 through 260 removed outlier: 4.673A pdb=" N MET A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 272 through 275 removed outlier: 3.951A pdb=" N ILE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.623A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.666A pdb=" N LYS A 368 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 543 through 548 removed outlier: 4.383A pdb=" N TYR A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 603 removed outlier: 3.825A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 647 through 678 removed outlier: 3.562A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 735 through 744 Processing helix chain 'A' and resid 754 through 765 removed outlier: 3.552A pdb=" N LYS A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 835 through 862 removed outlier: 3.524A pdb=" N MET A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.644A pdb=" N SER B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 4.318A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.877A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.545A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.682A pdb=" N VAL B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 263 " --> pdb=" O SER B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing helix chain 'B' and resid 288 through 310 Processing helix chain 'B' and resid 328 through 339 removed outlier: 3.618A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.788A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.619A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 581 removed outlier: 5.006A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER B 581 " --> pdb=" O PHE B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.703A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 654 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 Processing helix chain 'B' and resid 690 through 696 Processing helix chain 'B' and resid 700 through 706 removed outlier: 3.519A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 710 removed outlier: 3.897A pdb=" N ASN B 710 " --> pdb=" O GLY B 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 773 through 787 Processing helix chain 'B' and resid 788 through 797 Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 818 through 837 Processing helix chain 'B' and resid 839 through 844 removed outlier: 3.760A pdb=" N TYR B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.679A pdb=" N GLU C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 143 through 159 removed outlier: 3.878A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 245 through 260 removed outlier: 4.652A pdb=" N MET C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 272 through 275 removed outlier: 3.879A pdb=" N ILE C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.810A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.748A pdb=" N LYS C 368 " --> pdb=" O GLY C 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 369 " --> pdb=" O ASP C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 369' Processing helix chain 'C' and resid 478 through 491 Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 543 through 548 removed outlier: 4.369A pdb=" N TYR C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 601 removed outlier: 3.823A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 647 through 678 removed outlier: 3.591A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE C 652 " --> pdb=" O PHE C 648 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 735 through 744 Processing helix chain 'C' and resid 754 through 765 removed outlier: 3.660A pdb=" N LYS C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 803 Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 835 through 862 removed outlier: 3.507A pdb=" N MET C 839 " --> pdb=" O ALA C 835 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 857 " --> pdb=" O PHE C 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.645A pdb=" N SER D 90 " --> pdb=" O CYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 117 removed outlier: 4.317A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 179 through 191 removed outlier: 3.877A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 220 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.545A pdb=" N SER D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.682A pdb=" N VAL D 262 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 263 " --> pdb=" O SER D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 263' Processing helix chain 'D' and resid 288 through 310 Processing helix chain 'D' and resid 328 through 339 removed outlier: 3.618A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.788A 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 removed outlier: 3.620A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 581 removed outlier: 5.006A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL D 569 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 572 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER D 581 " --> pdb=" O PHE D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.703A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 654 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 674 through 677 Processing helix chain 'D' and resid 690 through 696 Processing helix chain 'D' and resid 700 through 706 removed outlier: 3.519A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 710 removed outlier: 3.898A pdb=" N ASN D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 707 through 710' Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 773 through 787 Processing helix chain 'D' and resid 788 through 797 Processing helix chain 'D' and resid 815 through 817 No H-bonds generated for 'chain 'D' and resid 815 through 817' Processing helix chain 'D' and resid 818 through 837 Processing helix chain 'D' and resid 839 through 844 removed outlier: 3.759A pdb=" N TYR D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 7.679A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 30 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 217 removed outlier: 7.604A pdb=" N ILE A 163 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 215 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 165 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN A 217 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 167 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 292 removed outlier: 4.920A pdb=" N GLY A 386 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 5.921A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET A 533 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AA7, first strand: chain 'A' and resid 702 through 703 removed outlier: 3.674A pdb=" N ALA A 703 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 751 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 42 removed outlier: 6.281A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.998A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 202 removed outlier: 6.964A pdb=" N PHE B 169 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU B 201 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP B 256 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 277 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 367 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 366 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.523A pdb=" N LEU B 406 " --> pdb=" O THR B 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AB4, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 524 through 525 removed outlier: 3.504A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 766 " --> pdb=" O ASP B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 530 through 532 Processing sheet with id=AB7, first strand: chain 'B' and resid 534 through 537 removed outlier: 6.218A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 65 through 66 removed outlier: 7.689A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY C 30 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 211 through 217 removed outlier: 7.643A pdb=" N ILE C 163 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL C 215 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 165 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN C 217 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 167 " --> pdb=" O GLN C 217 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL C 239 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 289 through 292 removed outlier: 4.848A pdb=" N GLY C 386 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 496 through 498 removed outlier: 5.894A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET C 533 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ALA C 536 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY C 780 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 432 through 433 Processing sheet with id=AC4, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AC5, first strand: chain 'C' and resid 702 through 703 removed outlier: 3.673A pdb=" N ALA C 703 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 751 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.281A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 123 through 124 removed outlier: 6.999A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 199 through 202 removed outlier: 6.964A pdb=" N PHE D 169 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU D 201 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP D 256 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU D 277 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU D 367 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 366 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 405 through 406 removed outlier: 3.522A pdb=" N LEU D 406 " --> pdb=" O THR D 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 408 through 409 Processing sheet with id=AD2, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 524 through 525 removed outlier: 3.503A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE D 766 " --> pdb=" O ASP D 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AD5, first strand: chain 'D' and resid 534 through 537 removed outlier: 6.219A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2667 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3918 1.31 - 1.44: 6372 1.44 - 1.57: 13338 1.57 - 1.70: 4 1.70 - 1.83: 240 Bond restraints: 23872 Sorted by residual: bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.851 1.591 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.851 1.591 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" O3 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.629 1.472 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" O3 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.629 1.474 0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 1.347 1.476 -0.129 2.00e-02 2.50e+03 4.15e+01 ... (remaining 23867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 31607 2.42 - 4.85: 843 4.85 - 7.27: 126 7.27 - 9.69: 12 9.69 - 12.12: 2 Bond angle restraints: 32590 Sorted by residual: angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.20 108.26 4.94 9.60e-01 1.09e+00 2.65e+01 angle pdb=" N VAL A 225 " pdb=" CA VAL A 225 " pdb=" C VAL A 225 " ideal model delta sigma weight residual 113.20 108.28 4.92 9.60e-01 1.09e+00 2.62e+01 angle pdb=" N HIS B 802 " pdb=" CA HIS B 802 " pdb=" C HIS B 802 " ideal model delta sigma weight residual 113.88 108.32 5.56 1.23e+00 6.61e-01 2.04e+01 angle pdb=" N HIS D 802 " pdb=" CA HIS D 802 " pdb=" C HIS D 802 " ideal model delta sigma weight residual 113.88 108.41 5.47 1.23e+00 6.61e-01 1.98e+01 angle pdb=" C GLN C 378 " pdb=" N ASN C 379 " pdb=" CA ASN C 379 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 ... (remaining 32585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 13163 23.29 - 46.58: 844 46.58 - 69.86: 133 69.86 - 93.15: 32 93.15 - 116.44: 14 Dihedral angle restraints: 14186 sinusoidal: 5168 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS D 746 " pdb=" SG CYS D 746 " pdb=" SG CYS D 801 " pdb=" CB CYS D 801 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS B 746 " pdb=" SG CYS B 746 " pdb=" SG CYS B 801 " pdb=" CB CYS B 801 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS A 441 " pdb=" SG CYS A 441 " pdb=" SG CYS A 475 " pdb=" CB CYS A 475 " ideal model delta sinusoidal sigma weight residual 93.00 33.79 59.21 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 14183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3756 0.119 - 0.238: 100 0.238 - 0.357: 2 0.357 - 0.476: 2 0.476 - 0.595: 2 Chirality restraints: 3862 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" CG LEU A 119 " pdb=" CB LEU A 119 " pdb=" CD1 LEU A 119 " pdb=" CD2 LEU A 119 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.59 2.00e-01 2.50e+01 8.85e+00 ... (remaining 3859 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 128 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY B 128 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY B 128 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 129 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 128 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY D 128 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY D 128 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 700 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C ALA B 700 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 700 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 701 " -0.013 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 702 2.66 - 3.22: 25378 3.22 - 3.78: 34842 3.78 - 4.34: 43763 4.34 - 4.90: 68264 Nonbonded interactions: 172949 Sorted by model distance: nonbonded pdb=" NH2 ARG A 233 " pdb=" O MET A 258 " model vdw 2.095 3.120 nonbonded pdb=" NH2 ARG C 233 " pdb=" O MET C 258 " model vdw 2.105 3.120 nonbonded pdb=" O MET B 829 " pdb=" OG SER B 832 " model vdw 2.137 3.040 nonbonded pdb=" O MET D 829 " pdb=" OG SER D 832 " model vdw 2.138 3.040 nonbonded pdb=" O LYS B 380 " pdb=" OG SER B 383 " model vdw 2.166 3.040 ... (remaining 172944 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.010 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.940 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.009 0.260 23902 Z= 0.435 Angle : 1.011 36.585 32662 Z= 0.534 Chirality : 0.054 0.595 3862 Planarity : 0.005 0.049 4134 Dihedral : 16.309 116.438 8308 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 18.01 % Favored : 81.79 % Rotamer: Outliers : 0.72 % Allowed : 11.62 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.87 (0.12), residues: 3076 helix: -2.02 (0.12), residues: 1176 sheet: -3.78 (0.20), residues: 366 loop : -4.20 (0.12), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 375 TYR 0.023 0.002 TYR C 816 PHE 0.020 0.002 PHE B 99 TRP 0.032 0.002 TRP A 268 HIS 0.009 0.002 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00910 (23872) covalent geometry : angle 0.94764 (32590) SS BOND : bond 0.00713 ( 18) SS BOND : angle 2.23627 ( 36) hydrogen bonds : bond 0.18535 ( 914) hydrogen bonds : angle 7.86094 ( 2667) link_BETA1-4 : bond 0.06412 ( 2) link_BETA1-4 : angle 23.61657 ( 6) link_NAG-ASN : bond 0.00474 ( 10) link_NAG-ASN : angle 4.50847 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 317 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 655 MET cc_start: 0.7127 (tmm) cc_final: 0.6878 (tmm) REVERT: A 662 MET cc_start: 0.9031 (tmm) cc_final: 0.8802 (tmm) REVERT: B 632 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8308 (t) REVERT: B 818 MET cc_start: 0.7685 (mpp) cc_final: 0.7255 (mtm) REVERT: C 258 MET cc_start: 0.6779 (tmm) cc_final: 0.6401 (tmm) REVERT: D 73 MET cc_start: 0.7493 (mtt) cc_final: 0.7122 (mtt) REVERT: D 139 GLU cc_start: 0.6173 (mm-30) cc_final: 0.5910 (mm-30) REVERT: D 142 MET cc_start: 0.6951 (tpp) cc_final: 0.6749 (mmt) REVERT: D 562 MET cc_start: 0.7615 (ppp) cc_final: 0.7334 (ppp) REVERT: D 632 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8476 (t) REVERT: D 818 MET cc_start: 0.7123 (mpp) cc_final: 0.6515 (mtm) outliers start: 17 outliers final: 5 residues processed: 333 average time/residue: 0.1348 time to fit residues: 74.8395 Evaluate side-chains 225 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 146 HIS A 161 ASN A 291 GLN A 707 GLN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 745 ASN B 127 HIS B 656 GLN B 767 GLN C 47 ASN C 146 HIS C 161 ASN C 291 GLN C 707 GLN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 745 ASN C 763 GLN D 127 HIS D 656 GLN D 767 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086272 restraints weight = 71164.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089364 restraints weight = 41709.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089715 restraints weight = 27713.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.089914 restraints weight = 22698.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090045 restraints weight = 21809.989| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23902 Z= 0.187 Angle : 0.766 12.220 32662 Z= 0.394 Chirality : 0.050 0.593 3862 Planarity : 0.005 0.059 4134 Dihedral : 10.557 107.231 3580 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 2.38 % Allowed : 16.34 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.14), residues: 3076 helix: -0.38 (0.14), residues: 1208 sheet: -2.62 (0.24), residues: 342 loop : -3.68 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 716 TYR 0.013 0.001 TYR D 282 PHE 0.018 0.002 PHE B 614 TRP 0.021 0.002 TRP D 197 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00426 (23872) covalent geometry : angle 0.74888 (32590) SS BOND : bond 0.00509 ( 18) SS BOND : angle 1.71023 ( 36) hydrogen bonds : bond 0.06041 ( 914) hydrogen bonds : angle 5.75747 ( 2667) link_BETA1-4 : bond 0.00087 ( 2) link_BETA1-4 : angle 5.49088 ( 6) link_NAG-ASN : bond 0.00578 ( 10) link_NAG-ASN : angle 4.40193 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8391 (ppp) cc_final: 0.6940 (mmt) REVERT: A 375 MET cc_start: 0.6877 (tpp) cc_final: 0.6587 (tpp) REVERT: A 385 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8041 (t) REVERT: A 662 MET cc_start: 0.9514 (tmm) cc_final: 0.9185 (tmm) REVERT: B 73 MET cc_start: 0.6731 (mtt) cc_final: 0.6524 (ptp) REVERT: B 105 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6981 (pm20) REVERT: B 308 LEU cc_start: 0.6908 (mm) cc_final: 0.5702 (pp) REVERT: B 786 ASP cc_start: 0.8357 (t0) cc_final: 0.8112 (t0) REVERT: B 818 MET cc_start: 0.8721 (mpp) cc_final: 0.8161 (mtm) REVERT: C 248 ASP cc_start: 0.7995 (m-30) cc_final: 0.7746 (m-30) REVERT: C 491 MET cc_start: 0.8355 (mtp) cc_final: 0.8133 (mtp) REVERT: C 597 MET cc_start: 0.8479 (mmm) cc_final: 0.8117 (ttt) REVERT: C 662 MET cc_start: 0.9508 (tmm) cc_final: 0.9270 (tmm) REVERT: C 783 MET cc_start: 0.7358 (mtm) cc_final: 0.7115 (mtm) REVERT: D 73 MET cc_start: 0.7007 (mtt) cc_final: 0.6736 (mtt) REVERT: D 101 ASP cc_start: 0.8918 (t0) cc_final: 0.8700 (t0) REVERT: D 142 MET cc_start: 0.7680 (tpp) cc_final: 0.7371 (mmt) REVERT: D 786 ASP cc_start: 0.8654 (t0) cc_final: 0.8448 (t0) REVERT: D 818 MET cc_start: 0.8654 (mpp) cc_final: 0.7920 (mtm) outliers start: 56 outliers final: 32 residues processed: 329 average time/residue: 0.1191 time to fit residues: 68.4330 Evaluate side-chains 271 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 831 CYS Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 138 optimal weight: 0.1980 chunk 105 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085432 restraints weight = 70849.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.086308 restraints weight = 42306.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087082 restraints weight = 33938.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087366 restraints weight = 28087.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087525 restraints weight = 26059.608| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23902 Z= 0.209 Angle : 0.767 12.137 32662 Z= 0.391 Chirality : 0.050 0.641 3862 Planarity : 0.005 0.053 4134 Dihedral : 9.703 99.320 3576 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 4.21 % Allowed : 18.38 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.15), residues: 3076 helix: 0.17 (0.15), residues: 1208 sheet: -2.23 (0.28), residues: 304 loop : -3.48 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.015 0.001 TYR B 282 PHE 0.019 0.002 PHE B 99 TRP 0.033 0.002 TRP B 197 HIS 0.004 0.001 HIS C 801 Details of bonding type rmsd covalent geometry : bond 0.00478 (23872) covalent geometry : angle 0.75117 (32590) SS BOND : bond 0.00625 ( 18) SS BOND : angle 2.09093 ( 36) hydrogen bonds : bond 0.05358 ( 914) hydrogen bonds : angle 5.58436 ( 2667) link_BETA1-4 : bond 0.00740 ( 2) link_BETA1-4 : angle 4.23272 ( 6) link_NAG-ASN : bond 0.00449 ( 10) link_NAG-ASN : angle 4.34827 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 252 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.4957 (OUTLIER) cc_final: 0.4656 (t0) REVERT: A 347 MET cc_start: 0.8517 (ppp) cc_final: 0.7038 (mmt) REVERT: A 375 MET cc_start: 0.6910 (tpp) cc_final: 0.6532 (tpp) REVERT: A 385 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8105 (t) REVERT: A 579 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: A 662 MET cc_start: 0.9509 (tmm) cc_final: 0.9142 (tmm) REVERT: A 806 MET cc_start: 0.9100 (tpp) cc_final: 0.8502 (mpp) REVERT: B 308 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.5958 (pp) REVERT: B 786 ASP cc_start: 0.8185 (t0) cc_final: 0.7853 (t0) REVERT: B 818 MET cc_start: 0.8777 (mpp) cc_final: 0.8058 (mtt) REVERT: C 248 ASP cc_start: 0.7981 (m-30) cc_final: 0.7680 (m-30) REVERT: C 385 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.8040 (t) REVERT: C 579 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7180 (m-10) REVERT: C 597 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8128 (ttt) REVERT: C 662 MET cc_start: 0.9471 (tmm) cc_final: 0.9232 (tmm) REVERT: C 783 MET cc_start: 0.7332 (mtm) cc_final: 0.6926 (mtm) REVERT: D 105 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: D 142 MET cc_start: 0.7660 (tpp) cc_final: 0.7396 (mmt) REVERT: D 200 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8316 (mm-30) REVERT: D 565 MET cc_start: 0.8496 (tpp) cc_final: 0.8191 (tpp) REVERT: D 788 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7662 (mm-30) REVERT: D 818 MET cc_start: 0.8436 (mpp) cc_final: 0.7912 (mtt) REVERT: D 829 MET cc_start: 0.8877 (mtm) cc_final: 0.8610 (mtm) outliers start: 99 outliers final: 60 residues processed: 331 average time/residue: 0.1159 time to fit residues: 67.3348 Evaluate side-chains 306 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 238 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 201 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 242 optimal weight: 0.0970 chunk 300 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 513 ASN A 695 ASN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 ASN ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 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 = 0.3620 r_free = 0.3620 target = 0.101738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083657 restraints weight = 72795.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085868 restraints weight = 43939.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086382 restraints weight = 31608.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086642 restraints weight = 26512.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086807 restraints weight = 24950.102| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 23902 Z= 0.254 Angle : 0.791 11.830 32662 Z= 0.405 Chirality : 0.050 0.679 3862 Planarity : 0.005 0.054 4134 Dihedral : 9.291 85.478 3576 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 5.11 % Allowed : 20.34 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.15), residues: 3076 helix: 0.40 (0.15), residues: 1194 sheet: -2.18 (0.28), residues: 316 loop : -3.40 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 815 TYR 0.018 0.002 TYR B 282 PHE 0.026 0.002 PHE D 99 TRP 0.024 0.002 TRP C 268 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00582 (23872) covalent geometry : angle 0.77704 (32590) SS BOND : bond 0.00515 ( 18) SS BOND : angle 2.01505 ( 36) hydrogen bonds : bond 0.05423 ( 914) hydrogen bonds : angle 5.55685 ( 2667) link_BETA1-4 : bond 0.00040 ( 2) link_BETA1-4 : angle 3.79418 ( 6) link_NAG-ASN : bond 0.00530 ( 10) link_NAG-ASN : angle 4.19824 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 251 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: A 597 MET cc_start: 0.8120 (ttt) cc_final: 0.7815 (ttt) REVERT: A 655 MET cc_start: 0.8461 (ttp) cc_final: 0.8211 (tmm) REVERT: A 662 MET cc_start: 0.9510 (tmm) cc_final: 0.9072 (tmm) REVERT: B 105 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: B 308 LEU cc_start: 0.7223 (mm) cc_final: 0.5897 (pp) REVERT: B 568 ILE cc_start: 0.9290 (mt) cc_final: 0.9051 (mm) REVERT: B 788 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 818 MET cc_start: 0.8689 (mpp) cc_final: 0.8300 (mpp) REVERT: C 154 MET cc_start: 0.8317 (ttm) cc_final: 0.8111 (ttt) REVERT: C 248 ASP cc_start: 0.8013 (m-30) cc_final: 0.7690 (m-30) REVERT: C 579 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: C 662 MET cc_start: 0.9423 (tmm) cc_final: 0.9090 (tmm) REVERT: D 73 MET cc_start: 0.6791 (mtt) cc_final: 0.6423 (ptp) REVERT: D 105 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: D 142 MET cc_start: 0.7651 (tpp) cc_final: 0.7371 (mmt) REVERT: D 273 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8075 (t80) REVERT: D 783 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9080 (mt) REVERT: D 786 ASP cc_start: 0.8456 (t0) cc_final: 0.7655 (t0) REVERT: D 788 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7845 (mp0) REVERT: D 818 MET cc_start: 0.8512 (mpp) cc_final: 0.7897 (mtt) outliers start: 120 outliers final: 79 residues processed: 354 average time/residue: 0.1143 time to fit residues: 70.7871 Evaluate side-chains 326 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 241 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 284 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 200 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 45 optimal weight: 6.9990 chunk 176 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 HIS A 763 GLN C 726 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.105260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.087023 restraints weight = 71056.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091149 restraints weight = 39521.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091271 restraints weight = 22862.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091489 restraints weight = 19321.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091642 restraints weight = 18563.726| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23902 Z= 0.140 Angle : 0.707 11.125 32662 Z= 0.359 Chirality : 0.048 0.718 3862 Planarity : 0.004 0.054 4134 Dihedral : 8.302 61.052 3576 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 3.79 % Allowed : 22.60 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 3076 helix: 0.73 (0.15), residues: 1204 sheet: -2.13 (0.28), residues: 314 loop : -3.18 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.015 0.001 TYR B 179 PHE 0.011 0.001 PHE B 146 TRP 0.021 0.001 TRP D 285 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00314 (23872) covalent geometry : angle 0.69276 (32590) SS BOND : bond 0.00530 ( 18) SS BOND : angle 1.67212 ( 36) hydrogen bonds : bond 0.04467 ( 914) hydrogen bonds : angle 5.08207 ( 2667) link_BETA1-4 : bond 0.00384 ( 2) link_BETA1-4 : angle 3.22260 ( 6) link_NAG-ASN : bond 0.00579 ( 10) link_NAG-ASN : angle 4.09601 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 276 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7809 (mmm) cc_final: 0.7417 (mmp) REVERT: A 347 MET cc_start: 0.8374 (ppp) cc_final: 0.6834 (mmt) REVERT: A 375 MET cc_start: 0.7209 (tpp) cc_final: 0.6751 (tpp) REVERT: A 579 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7057 (m-10) REVERT: A 662 MET cc_start: 0.9461 (tmm) cc_final: 0.9225 (tmm) REVERT: B 37 ILE cc_start: 0.5301 (OUTLIER) cc_final: 0.4753 (mt) REVERT: B 105 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: B 308 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.5954 (pp) REVERT: B 565 MET cc_start: 0.8395 (tpp) cc_final: 0.8010 (tpp) REVERT: B 568 ILE cc_start: 0.9304 (mt) cc_final: 0.9072 (mm) REVERT: B 656 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7730 (mm-40) REVERT: B 786 ASP cc_start: 0.8388 (t0) cc_final: 0.7546 (t0) REVERT: B 788 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8241 (mp0) REVERT: B 818 MET cc_start: 0.8696 (mpp) cc_final: 0.8372 (mpp) REVERT: C 248 ASP cc_start: 0.8000 (m-30) cc_final: 0.7687 (m-30) REVERT: C 579 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: C 662 MET cc_start: 0.9409 (tmm) cc_final: 0.9160 (tmm) REVERT: C 783 MET cc_start: 0.7560 (mtm) cc_final: 0.7198 (mtm) REVERT: C 806 MET cc_start: 0.8810 (mmm) cc_final: 0.8351 (mmm) REVERT: D 73 MET cc_start: 0.6510 (mtt) cc_final: 0.6204 (ptp) REVERT: D 105 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: D 142 MET cc_start: 0.7722 (tpp) cc_final: 0.7444 (mmt) REVERT: D 202 VAL cc_start: 0.9305 (t) cc_final: 0.8740 (p) REVERT: D 537 MET cc_start: 0.8346 (ttt) cc_final: 0.8099 (ttt) REVERT: D 656 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7666 (mm-40) REVERT: D 788 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7761 (mm-30) REVERT: D 818 MET cc_start: 0.8527 (mpp) cc_final: 0.7885 (mtt) outliers start: 89 outliers final: 52 residues processed: 350 average time/residue: 0.1252 time to fit residues: 76.3572 Evaluate side-chains 316 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 218 optimal weight: 7.9990 chunk 176 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086205 restraints weight = 71569.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088430 restraints weight = 40253.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089028 restraints weight = 27723.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089359 restraints weight = 24560.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089590 restraints weight = 23263.793| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23902 Z= 0.169 Angle : 0.725 11.676 32662 Z= 0.366 Chirality : 0.049 0.926 3862 Planarity : 0.004 0.058 4134 Dihedral : 7.507 55.580 3574 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 4.55 % Allowed : 23.11 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 3076 helix: 0.78 (0.15), residues: 1200 sheet: -2.11 (0.28), residues: 314 loop : -3.08 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 692 TYR 0.019 0.001 TYR D 179 PHE 0.013 0.001 PHE B 614 TRP 0.020 0.001 TRP D 285 HIS 0.004 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00387 (23872) covalent geometry : angle 0.71104 (32590) SS BOND : bond 0.00354 ( 18) SS BOND : angle 1.79071 ( 36) hydrogen bonds : bond 0.04643 ( 914) hydrogen bonds : angle 5.14591 ( 2667) link_BETA1-4 : bond 0.00518 ( 2) link_BETA1-4 : angle 2.80467 ( 6) link_NAG-ASN : bond 0.00545 ( 10) link_NAG-ASN : angle 4.12984 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 260 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8444 (ppp) cc_final: 0.7023 (mmt) REVERT: A 375 MET cc_start: 0.6734 (tpp) cc_final: 0.6409 (tpp) REVERT: A 576 MET cc_start: 0.8353 (mtp) cc_final: 0.8079 (mmm) REVERT: A 579 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7101 (m-10) REVERT: A 662 MET cc_start: 0.9482 (tmm) cc_final: 0.9171 (tmm) REVERT: A 806 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8824 (mmt) REVERT: B 105 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: B 139 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7843 (mp0) REVERT: B 308 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.5943 (pp) REVERT: B 565 MET cc_start: 0.8433 (tpp) cc_final: 0.8174 (tpp) REVERT: B 568 ILE cc_start: 0.9315 (mt) cc_final: 0.9103 (mm) REVERT: B 656 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7702 (mm-40) REVERT: B 818 MET cc_start: 0.8652 (mpp) cc_final: 0.8350 (mpp) REVERT: C 248 ASP cc_start: 0.8062 (m-30) cc_final: 0.7660 (m-30) REVERT: C 579 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7039 (m-10) REVERT: C 662 MET cc_start: 0.9431 (tmm) cc_final: 0.9167 (tmm) REVERT: C 783 MET cc_start: 0.7523 (mtm) cc_final: 0.7133 (mtm) REVERT: D 73 MET cc_start: 0.6465 (mtt) cc_final: 0.6127 (ptp) REVERT: D 105 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: D 142 MET cc_start: 0.7729 (tpp) cc_final: 0.7457 (mmt) REVERT: D 308 LEU cc_start: 0.6912 (mm) cc_final: 0.5776 (pp) REVERT: D 786 ASP cc_start: 0.8490 (t0) cc_final: 0.7549 (t0) REVERT: D 818 MET cc_start: 0.8555 (mpp) cc_final: 0.7896 (mtt) outliers start: 107 outliers final: 73 residues processed: 345 average time/residue: 0.1233 time to fit residues: 74.4273 Evaluate side-chains 324 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 244 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 150 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 0.0370 chunk 298 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 297 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 177 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.107682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.090076 restraints weight = 71047.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093833 restraints weight = 41140.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.093932 restraints weight = 25399.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094176 restraints weight = 21012.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094351 restraints weight = 20165.513| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23902 Z= 0.118 Angle : 0.677 12.822 32662 Z= 0.340 Chirality : 0.047 0.688 3862 Planarity : 0.004 0.057 4134 Dihedral : 6.788 55.549 3574 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.53 % Allowed : 24.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 3076 helix: 0.96 (0.15), residues: 1188 sheet: -1.99 (0.29), residues: 290 loop : -2.86 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 784 TYR 0.019 0.001 TYR D 179 PHE 0.012 0.001 PHE C 42 TRP 0.025 0.001 TRP D 285 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00258 (23872) covalent geometry : angle 0.66614 (32590) SS BOND : bond 0.00293 ( 18) SS BOND : angle 1.49126 ( 36) hydrogen bonds : bond 0.03922 ( 914) hydrogen bonds : angle 4.84951 ( 2667) link_BETA1-4 : bond 0.00540 ( 2) link_BETA1-4 : angle 2.71503 ( 6) link_NAG-ASN : bond 0.00713 ( 10) link_NAG-ASN : angle 3.66488 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 280 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8370 (ppp) cc_final: 0.6941 (mmt) REVERT: A 375 MET cc_start: 0.6860 (tpp) cc_final: 0.6508 (tpp) REVERT: A 579 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7145 (m-10) REVERT: A 662 MET cc_start: 0.9389 (tmm) cc_final: 0.9157 (tmm) REVERT: B 105 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: B 307 MET cc_start: 0.5340 (tpp) cc_final: 0.4341 (tpp) REVERT: B 308 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5952 (pp) REVERT: B 337 ARG cc_start: 0.8692 (tpt90) cc_final: 0.8332 (tpt90) REVERT: B 565 MET cc_start: 0.8311 (tpp) cc_final: 0.8110 (tpp) REVERT: B 568 ILE cc_start: 0.9249 (mt) cc_final: 0.9025 (mm) REVERT: B 656 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7859 (mm-40) REVERT: B 818 MET cc_start: 0.8515 (mpp) cc_final: 0.8261 (mpp) REVERT: C 248 ASP cc_start: 0.7705 (m-30) cc_final: 0.7451 (m-30) REVERT: C 579 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7103 (m-10) REVERT: C 655 MET cc_start: 0.7345 (ttp) cc_final: 0.6925 (ttp) REVERT: C 723 MET cc_start: 0.9037 (mtm) cc_final: 0.8713 (ttm) REVERT: C 783 MET cc_start: 0.7279 (mtm) cc_final: 0.6879 (mtm) REVERT: C 851 LEU cc_start: 0.9073 (mt) cc_final: 0.8863 (mp) REVERT: D 105 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: D 142 MET cc_start: 0.7668 (tpp) cc_final: 0.7446 (mmt) REVERT: D 143 PHE cc_start: 0.8155 (t80) cc_final: 0.7279 (t80) REVERT: D 308 LEU cc_start: 0.6416 (mm) cc_final: 0.5900 (pp) REVERT: D 337 ARG cc_start: 0.8792 (tpt90) cc_final: 0.8477 (tpt90) REVERT: D 656 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7727 (mm-40) REVERT: D 789 MET cc_start: 0.8902 (mmm) cc_final: 0.8689 (mmm) REVERT: D 818 MET cc_start: 0.8398 (mpp) cc_final: 0.7690 (mtt) outliers start: 83 outliers final: 61 residues processed: 350 average time/residue: 0.1226 time to fit residues: 74.2149 Evaluate side-chains 333 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 242 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 292 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 43 optimal weight: 0.2980 chunk 131 optimal weight: 0.7980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.105765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087862 restraints weight = 71202.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090833 restraints weight = 41139.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091203 restraints weight = 28273.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091477 restraints weight = 23014.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091607 restraints weight = 21905.296| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23902 Z= 0.157 Angle : 0.708 12.456 32662 Z= 0.354 Chirality : 0.048 1.006 3862 Planarity : 0.004 0.060 4134 Dihedral : 6.679 55.764 3574 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 3.87 % Allowed : 24.34 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.15), residues: 3076 helix: 0.94 (0.15), residues: 1204 sheet: -1.99 (0.30), residues: 272 loop : -2.79 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 544 TYR 0.018 0.001 TYR D 179 PHE 0.012 0.001 PHE B 99 TRP 0.024 0.001 TRP D 285 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00356 (23872) covalent geometry : angle 0.69697 (32590) SS BOND : bond 0.00228 ( 18) SS BOND : angle 1.53274 ( 36) hydrogen bonds : bond 0.04304 ( 914) hydrogen bonds : angle 4.91739 ( 2667) link_BETA1-4 : bond 0.00339 ( 2) link_BETA1-4 : angle 2.73021 ( 6) link_NAG-ASN : bond 0.00598 ( 10) link_NAG-ASN : angle 3.61086 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 269 time to evaluate : 0.807 Fit side-chains REVERT: A 347 MET cc_start: 0.8470 (ppp) cc_final: 0.7112 (mmt) REVERT: A 375 MET cc_start: 0.6891 (tpp) cc_final: 0.6559 (tpp) REVERT: A 579 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: A 662 MET cc_start: 0.9428 (tmm) cc_final: 0.9155 (tmm) REVERT: B 105 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: B 143 PHE cc_start: 0.8079 (t80) cc_final: 0.7404 (t80) REVERT: B 307 MET cc_start: 0.5688 (tpp) cc_final: 0.4774 (tpp) REVERT: B 308 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.5832 (pp) REVERT: B 337 ARG cc_start: 0.8743 (tpt90) cc_final: 0.8404 (tpt90) REVERT: B 568 ILE cc_start: 0.9269 (mt) cc_final: 0.9020 (mm) REVERT: B 656 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7899 (mm-40) REVERT: B 818 MET cc_start: 0.8539 (mpp) cc_final: 0.8244 (mpp) REVERT: C 248 ASP cc_start: 0.7885 (m-30) cc_final: 0.7639 (m-30) REVERT: C 579 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: C 597 MET cc_start: 0.8088 (ttt) cc_final: 0.7864 (ttm) REVERT: C 629 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.8420 (m-10) REVERT: C 655 MET cc_start: 0.7463 (ttp) cc_final: 0.7131 (ttp) REVERT: C 783 MET cc_start: 0.7299 (mtm) cc_final: 0.6913 (mtm) REVERT: D 105 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: D 142 MET cc_start: 0.7683 (tpp) cc_final: 0.7465 (mmt) REVERT: D 143 PHE cc_start: 0.8370 (t80) cc_final: 0.7450 (t80) REVERT: D 308 LEU cc_start: 0.6529 (mm) cc_final: 0.5960 (pp) REVERT: D 337 ARG cc_start: 0.8808 (tpt90) cc_final: 0.8486 (tpt90) REVERT: D 656 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7744 (mm-40) REVERT: D 818 MET cc_start: 0.8466 (mpp) cc_final: 0.8238 (mpp) outliers start: 91 outliers final: 72 residues processed: 341 average time/residue: 0.1233 time to fit residues: 72.9602 Evaluate side-chains 341 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 261 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 150 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 303 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.105465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087687 restraints weight = 71422.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.089649 restraints weight = 41736.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090161 restraints weight = 30117.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090466 restraints weight = 26775.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090731 restraints weight = 25368.853| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23902 Z= 0.165 Angle : 0.721 11.570 32662 Z= 0.359 Chirality : 0.049 0.986 3862 Planarity : 0.004 0.059 4134 Dihedral : 6.641 55.690 3574 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 3.91 % Allowed : 24.47 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.15), residues: 3076 helix: 0.90 (0.15), residues: 1208 sheet: -2.11 (0.28), residues: 318 loop : -2.74 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.017 0.001 TYR D 179 PHE 0.011 0.001 PHE B 614 TRP 0.031 0.001 TRP D 285 HIS 0.003 0.001 HIS D 486 Details of bonding type rmsd covalent geometry : bond 0.00377 (23872) covalent geometry : angle 0.71092 (32590) SS BOND : bond 0.00241 ( 18) SS BOND : angle 1.60719 ( 36) hydrogen bonds : bond 0.04346 ( 914) hydrogen bonds : angle 4.95004 ( 2667) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 2.79482 ( 6) link_NAG-ASN : bond 0.00594 ( 10) link_NAG-ASN : angle 3.54494 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 268 time to evaluate : 0.921 Fit side-chains REVERT: A 347 MET cc_start: 0.8455 (ppp) cc_final: 0.7107 (mmt) REVERT: A 375 MET cc_start: 0.6924 (tpp) cc_final: 0.6567 (tpp) REVERT: A 579 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7205 (m-10) REVERT: A 662 MET cc_start: 0.9432 (tmm) cc_final: 0.9162 (tmm) REVERT: A 806 MET cc_start: 0.9163 (mmm) cc_final: 0.8358 (mmt) REVERT: B 105 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: B 143 PHE cc_start: 0.8091 (t80) cc_final: 0.7518 (t80) REVERT: B 307 MET cc_start: 0.5737 (tpp) cc_final: 0.4902 (tpp) REVERT: B 308 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.5999 (pp) REVERT: B 337 ARG cc_start: 0.8748 (tpt90) cc_final: 0.8429 (tpt90) REVERT: B 568 ILE cc_start: 0.9274 (mt) cc_final: 0.9063 (mm) REVERT: B 656 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7890 (mm-40) REVERT: B 818 MET cc_start: 0.8561 (mpp) cc_final: 0.8273 (mpp) REVERT: C 248 ASP cc_start: 0.7921 (m-30) cc_final: 0.7687 (m-30) REVERT: C 579 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: C 629 TRP cc_start: 0.8715 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: C 655 MET cc_start: 0.7504 (ttp) cc_final: 0.7130 (ttp) REVERT: C 783 MET cc_start: 0.7312 (mtm) cc_final: 0.6909 (mtm) REVERT: D 105 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: D 142 MET cc_start: 0.7708 (tpp) cc_final: 0.7496 (mmt) REVERT: D 143 PHE cc_start: 0.8379 (t80) cc_final: 0.7459 (t80) REVERT: D 308 LEU cc_start: 0.6514 (mm) cc_final: 0.5702 (tt) REVERT: D 337 ARG cc_start: 0.8704 (tpt90) cc_final: 0.8265 (tpt90) REVERT: D 656 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7932 (mm-40) REVERT: D 818 MET cc_start: 0.8502 (mpp) cc_final: 0.7770 (mtt) outliers start: 92 outliers final: 78 residues processed: 343 average time/residue: 0.1254 time to fit residues: 74.6470 Evaluate side-chains 345 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 259 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 138 optimal weight: 0.0870 chunk 239 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 265 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 175 optimal weight: 0.0060 chunk 127 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.108710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.091032 restraints weight = 70527.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094646 restraints weight = 41191.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.094754 restraints weight = 26475.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.094908 restraints weight = 22520.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095335 restraints weight = 20914.140| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23902 Z= 0.119 Angle : 0.702 15.078 32662 Z= 0.344 Chirality : 0.047 0.875 3862 Planarity : 0.004 0.061 4134 Dihedral : 6.378 56.258 3574 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 3.11 % Allowed : 24.85 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.15), residues: 3076 helix: 1.03 (0.15), residues: 1194 sheet: -1.81 (0.29), residues: 304 loop : -2.62 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.019 0.001 TYR D 179 PHE 0.011 0.001 PHE C 42 TRP 0.031 0.001 TRP D 285 HIS 0.007 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00262 (23872) covalent geometry : angle 0.69269 (32590) SS BOND : bond 0.00284 ( 18) SS BOND : angle 1.44748 ( 36) hydrogen bonds : bond 0.03783 ( 914) hydrogen bonds : angle 4.78490 ( 2667) link_BETA1-4 : bond 0.00351 ( 2) link_BETA1-4 : angle 2.65975 ( 6) link_NAG-ASN : bond 0.00680 ( 10) link_NAG-ASN : angle 3.32887 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 283 time to evaluate : 0.566 Fit side-chains REVERT: A 235 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8902 (mm) REVERT: A 282 TYR cc_start: 0.7975 (m-80) cc_final: 0.7677 (m-10) REVERT: A 347 MET cc_start: 0.8455 (ppp) cc_final: 0.7032 (mmt) REVERT: A 375 MET cc_start: 0.6952 (tpp) cc_final: 0.6631 (tpp) REVERT: A 579 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7073 (m-10) REVERT: A 662 MET cc_start: 0.9389 (tmm) cc_final: 0.9143 (tmm) REVERT: A 806 MET cc_start: 0.9139 (mmm) cc_final: 0.8282 (mmt) REVERT: B 105 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: B 143 PHE cc_start: 0.7950 (t80) cc_final: 0.7422 (t80) REVERT: B 307 MET cc_start: 0.5427 (tpp) cc_final: 0.4832 (tpp) REVERT: B 308 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6075 (pp) REVERT: B 337 ARG cc_start: 0.8732 (tpt90) cc_final: 0.8432 (tpt90) REVERT: B 568 ILE cc_start: 0.9256 (mt) cc_final: 0.9052 (mm) REVERT: B 575 PHE cc_start: 0.8162 (p90) cc_final: 0.7257 (m-10) REVERT: B 656 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7789 (mm-40) REVERT: B 818 MET cc_start: 0.8482 (mpp) cc_final: 0.8218 (mpp) REVERT: C 248 ASP cc_start: 0.7805 (m-30) cc_final: 0.7590 (m-30) REVERT: C 579 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.6861 (m-10) REVERT: C 655 MET cc_start: 0.7380 (ttp) cc_final: 0.7106 (ttp) REVERT: C 733 GLU cc_start: 0.8109 (mp0) cc_final: 0.7618 (tp30) REVERT: C 783 MET cc_start: 0.7276 (mtm) cc_final: 0.6931 (mtm) REVERT: D 105 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: D 142 MET cc_start: 0.7631 (tpp) cc_final: 0.7409 (mmt) REVERT: D 143 PHE cc_start: 0.8213 (t80) cc_final: 0.7343 (t80) REVERT: D 308 LEU cc_start: 0.6574 (mm) cc_final: 0.6100 (tt) REVERT: D 337 ARG cc_start: 0.8691 (tpt90) cc_final: 0.8280 (tpt90) REVERT: D 656 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7897 (mm-40) REVERT: D 818 MET cc_start: 0.8360 (mpp) cc_final: 0.7634 (mtt) outliers start: 73 outliers final: 64 residues processed: 344 average time/residue: 0.1222 time to fit residues: 72.4122 Evaluate side-chains 337 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 265 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 189 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.108153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.090345 restraints weight = 70686.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.092732 restraints weight = 40615.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.093334 restraints weight = 27660.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093575 restraints weight = 23851.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.093897 restraints weight = 22888.465| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23902 Z= 0.125 Angle : 0.708 17.660 32662 Z= 0.346 Chirality : 0.047 0.798 3862 Planarity : 0.004 0.063 4134 Dihedral : 6.260 55.831 3574 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 3.32 % Allowed : 25.23 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.15), residues: 3076 helix: 1.08 (0.16), residues: 1206 sheet: -1.83 (0.29), residues: 306 loop : -2.58 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 337 TYR 0.018 0.001 TYR D 179 PHE 0.012 0.001 PHE B 143 TRP 0.033 0.001 TRP D 285 HIS 0.002 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00283 (23872) covalent geometry : angle 0.69878 (32590) SS BOND : bond 0.00247 ( 18) SS BOND : angle 1.44414 ( 36) hydrogen bonds : bond 0.03892 ( 914) hydrogen bonds : angle 4.79316 ( 2667) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 2.52266 ( 6) link_NAG-ASN : bond 0.00633 ( 10) link_NAG-ASN : angle 3.30385 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3123.78 seconds wall clock time: 54 minutes 51.37 seconds (3291.37 seconds total)