Starting phenix.real_space_refine on Sun Sep 13 11:54:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6whu_21676/09_2026/6whu_21676.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whu_21676/09_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_21676/09_2026/6whu_21676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whu_21676/09_2026/6whu_21676.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6whu_21676/09_2026/6whu_21676.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6whu_21676/09_2026/6whu_21676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6whu_21676/09_2026/6whu_21676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whu_21676/09_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 5.14, per 1000 atoms: 0.22 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: 1.99 Conformation dependent library (CDL) restraints added in 863.9 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: 0.74 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: 4.79 Time building geometry restraints manager: 2.62 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 - 17.92: 12382 17.92 - 35.84: 1245 35.84 - 53.76: 209 53.76 - 71.68: 44 71.68 - 89.60: 22 Dihedral angle restraints: 13902 sinusoidal: 4884 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 13899 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: 0.02 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: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.750 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 15.084 89.604 8024 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/Z covalent geometry : bond 0.00910 / 0.43 (23872) covalent geometry : angle 0.94764 / 0.52 (32590) SS BOND : bond 0.00713 / 0.59 ( 18) SS BOND : angle 2.23627 / 1.58 ( 36) hydrogen bonds : bond 0.18535 / 12.77 ( 914) hydrogen bonds : angle 7.86094 / 5.52 ( 2667) link_BETA1-4 : bond 0.06412 / 3.22 ( 2) link_BETA1-4 : angle 23.61657 / 13.42 ( 6) link_NAG-ASN : bond 0.00474 / 0.31 ( 10) link_NAG-ASN : angle 4.50847 / 3.41 ( 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 : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 640 ILE cc_start: 0.8369 (tp) cc_final: 0.8163 (tt) REVERT: A 655 MET cc_start: 0.7127 (tmm) cc_final: 0.6885 (tmm) REVERT: A 662 MET cc_start: 0.9031 (tmm) cc_final: 0.8803 (tmm) REVERT: B 632 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8322 (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: 0.6748 (mmt) REVERT: D 562 MET cc_start: 0.7615 (ppp) cc_final: 0.7333 (ppp) REVERT: D 632 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8478 (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: 0.1397 time to fit residues: 78.2268 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 : 0.905 ------------------------------------------------------------------------------- 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... 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 730 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 513 ASN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086336 restraints weight = 71090.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089443 restraints weight = 41563.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089796 restraints weight = 27530.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089988 restraints weight = 22523.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090122 restraints weight = 21642.091| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23902 Z= 0.180 Angle : 0.763 13.180 32662 Z= 0.395 Chirality : 0.050 0.564 3862 Planarity : 0.005 0.060 4134 Dihedral : 7.055 58.704 3296 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 2.43 % Allowed : 16.47 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.24 (0.14), residues: 3076 helix: -0.38 (0.14), residues: 1208 sheet: -2.73 (0.24), residues: 350 loop : -3.64 (0.14), residues: 1518 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 0.014 0.002 TRP B 197 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (23872) covalent geometry : angle 0.74807 / 0.39 (32590) SS BOND : bond 0.00529 / 0.40 ( 18) SS BOND : angle 1.63643 / 1.17 ( 36) hydrogen bonds : bond 0.05943 / 4.05 ( 914) hydrogen bonds : angle 5.76554 / 4.04 ( 2667) link_BETA1-4 : bond 0.00899 / 0.47 ( 2) link_BETA1-4 : angle 3.87551 / 2.09 ( 6) link_NAG-ASN : bond 0.00693 / 0.46 ( 10) link_NAG-ASN : angle 4.44666 / 3.49 ( 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 337 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8400 (ppp) cc_final: 0.6955 (mmt) REVERT: A 375 MET cc_start: 0.6850 (tpp) cc_final: 0.6540 (tpp) REVERT: A 385 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8060 (t) REVERT: A 597 MET cc_start: 0.8521 (mmm) cc_final: 0.8161 (ttt) REVERT: A 640 ILE cc_start: 0.9120 (tp) cc_final: 0.8826 (tt) REVERT: A 662 MET cc_start: 0.9519 (tmm) cc_final: 0.9161 (tmm) REVERT: B 73 MET cc_start: 0.6702 (mtt) cc_final: 0.6433 (ptp) REVERT: B 105 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: B 308 LEU cc_start: 0.6938 (mm) cc_final: 0.5724 (pp) REVERT: B 786 ASP cc_start: 0.8277 (t0) cc_final: 0.7995 (t0) REVERT: B 818 MET cc_start: 0.8780 (mpp) cc_final: 0.8254 (mtm) REVERT: C 248 ASP cc_start: 0.8038 (m-30) cc_final: 0.7790 (m-30) REVERT: C 491 MET cc_start: 0.8349 (mtp) cc_final: 0.8120 (mtp) REVERT: C 597 MET cc_start: 0.8545 (mmm) cc_final: 0.8161 (ttt) REVERT: C 662 MET cc_start: 0.9510 (tmm) cc_final: 0.9264 (tmm) REVERT: D 73 MET cc_start: 0.6971 (mtt) cc_final: 0.6677 (mtt) REVERT: D 101 ASP cc_start: 0.8939 (t0) cc_final: 0.8726 (t0) REVERT: D 142 MET cc_start: 0.7697 (tpp) cc_final: 0.7386 (mmt) REVERT: D 386 MET cc_start: 0.8426 (mmm) cc_final: 0.8084 (mmm) REVERT: D 786 ASP cc_start: 0.8557 (t0) cc_final: 0.8336 (t0) REVERT: D 818 MET cc_start: 0.8685 (mpp) cc_final: 0.7992 (mtm) outliers start: 57 outliers final: 34 residues processed: 327 average time/residue: 0.1278 time to fit residues: 72.7158 Evaluate side-chains 277 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 186 ILE 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: 2.9990 chunk 74 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 HIS A 513 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 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** 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 = 0.3640 r_free = 0.3640 target = 0.102792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084815 restraints weight = 72122.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.088788 restraints weight = 41727.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088796 restraints weight = 24652.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088996 restraints weight = 20794.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089119 restraints weight = 20112.036| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23902 Z= 0.206 Angle : 0.750 12.144 32662 Z= 0.385 Chirality : 0.048 0.259 3862 Planarity : 0.004 0.053 4134 Dihedral : 6.666 53.196 3292 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.30 % Favored : 86.70 % Rotamer: Outliers : 4.43 % Allowed : 18.47 % Favored : 77.11 % 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: -2.61 (0.15), residues: 3076 helix: 0.24 (0.15), residues: 1214 sheet: -2.15 (0.28), residues: 302 loop : -3.45 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 692 TYR 0.016 0.001 TYR B 282 PHE 0.019 0.002 PHE B 99 TRP 0.035 0.002 TRP B 197 HIS 0.005 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (23872) covalent geometry : angle 0.73632 / 0.38 (32590) SS BOND : bond 0.00436 / 0.28 ( 18) SS BOND : angle 1.72953 / 1.17 ( 36) hydrogen bonds : bond 0.05264 / 3.60 ( 914) hydrogen bonds : angle 5.47437 / 3.83 ( 2667) link_BETA1-4 : bond 0.00530 / 0.27 ( 2) link_BETA1-4 : angle 3.50911 / 1.91 ( 6) link_NAG-ASN : bond 0.00512 / 0.32 ( 10) link_NAG-ASN : angle 4.10394 / 3.22 ( 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 358 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 254 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASP cc_start: 0.5005 (OUTLIER) cc_final: 0.4679 (t0) REVERT: A 375 MET cc_start: 0.7114 (tpp) cc_final: 0.6668 (tpp) REVERT: A 579 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.6938 (m-10) REVERT: A 662 MET cc_start: 0.9498 (tmm) cc_final: 0.9091 (tmm) REVERT: A 806 MET cc_start: 0.9148 (tpp) cc_final: 0.8696 (mpp) REVERT: B 308 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.5974 (pp) REVERT: B 786 ASP cc_start: 0.8253 (t0) cc_final: 0.8035 (t0) REVERT: B 795 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9540 (tt) REVERT: B 818 MET cc_start: 0.8705 (mpp) cc_final: 0.8072 (mtt) REVERT: C 248 ASP cc_start: 0.7989 (m-30) cc_final: 0.7683 (m-30) REVERT: C 375 MET cc_start: 0.7279 (tpp) cc_final: 0.7070 (tpp) REVERT: C 579 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: C 662 MET cc_start: 0.9421 (tmm) cc_final: 0.9156 (tmm) REVERT: C 783 MET cc_start: 0.7441 (mtm) cc_final: 0.7041 (mtm) REVERT: D 105 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: D 142 MET cc_start: 0.7659 (tpp) cc_final: 0.7359 (mmt) REVERT: D 200 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8319 (mm-30) REVERT: D 788 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 818 MET cc_start: 0.8508 (mpp) cc_final: 0.7983 (mtt) outliers start: 104 outliers final: 66 residues processed: 336 average time/residue: 0.1283 time to fit residues: 75.3741 Evaluate side-chains 310 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 238 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 663 ILE 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 564 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 795 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 119 LEU 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 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 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 765 CYS Chi-restraints excluded: chain C residue 798 LEU Chi-restraints excluded: chain C residue 816 TYR 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 570 SER Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 655 ILE 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: 5.9990 chunk 255 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 300 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 234 optimal weight: 0.0020 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3685 r_free = 0.3685 target = 0.105636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087765 restraints weight = 71907.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.091311 restraints weight = 41822.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091530 restraints weight = 26099.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.091723 restraints weight = 21521.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.091890 restraints weight = 20822.707| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23902 Z= 0.136 Angle : 0.679 11.322 32662 Z= 0.348 Chirality : 0.047 0.314 3862 Planarity : 0.004 0.056 4134 Dihedral : 6.250 50.638 3292 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 3.49 % Allowed : 20.77 % Favored : 75.74 % 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: -2.21 (0.15), residues: 3076 helix: 0.63 (0.15), residues: 1216 sheet: -2.20 (0.27), residues: 324 loop : -3.21 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.010 0.001 TYR C 668 PHE 0.013 0.001 PHE D 614 TRP 0.018 0.001 TRP D 197 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (23872) covalent geometry : angle 0.66687 / 0.35 (32590) SS BOND : bond 0.00384 / 0.25 ( 18) SS BOND : angle 1.44189 / 0.96 ( 36) hydrogen bonds : bond 0.04486 / 3.09 ( 914) hydrogen bonds : angle 5.06714 / 3.54 ( 2667) link_BETA1-4 : bond 0.00781 / 0.39 ( 2) link_BETA1-4 : angle 2.76977 / 1.50 ( 6) link_NAG-ASN : bond 0.00616 / 0.40 ( 10) link_NAG-ASN : angle 3.81782 / 3.01 ( 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 363 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 281 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8370 (ppp) cc_final: 0.6869 (mmt) REVERT: A 375 MET cc_start: 0.6841 (tpp) cc_final: 0.6420 (tpp) REVERT: A 579 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.6864 (m-10) REVERT: A 662 MET cc_start: 0.9439 (tmm) cc_final: 0.9189 (tmm) REVERT: A 806 MET cc_start: 0.9098 (tpp) cc_final: 0.8892 (mpp) REVERT: B 105 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: B 308 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.5654 (pp) REVERT: B 562 MET cc_start: 0.8536 (tmm) cc_final: 0.8331 (tmm) REVERT: B 565 MET cc_start: 0.8308 (tpp) cc_final: 0.8054 (tpp) REVERT: B 631 MET cc_start: 0.8284 (tpt) cc_final: 0.7985 (tpp) REVERT: B 656 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7779 (mm-40) REVERT: B 788 GLU cc_start: 0.8704 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 818 MET cc_start: 0.8632 (mpp) cc_final: 0.8319 (mpp) REVERT: C 248 ASP cc_start: 0.7909 (m-30) cc_final: 0.7612 (m-30) REVERT: C 375 MET cc_start: 0.7185 (tpp) cc_final: 0.6930 (tpp) REVERT: C 579 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7067 (m-10) REVERT: C 783 MET cc_start: 0.7386 (mtm) cc_final: 0.7091 (mtm) REVERT: D 73 MET cc_start: 0.6718 (mtt) cc_final: 0.6274 (ptp) REVERT: D 105 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: D 142 MET cc_start: 0.7674 (tpp) cc_final: 0.7422 (mmt) REVERT: D 308 LEU cc_start: 0.6771 (mm) cc_final: 0.5695 (pp) REVERT: D 565 MET cc_start: 0.8014 (tpp) cc_final: 0.7803 (tpp) REVERT: D 656 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7778 (mm-40) REVERT: D 818 MET cc_start: 0.8422 (mpp) cc_final: 0.7791 (mtt) outliers start: 82 outliers final: 46 residues processed: 346 average time/residue: 0.1279 time to fit residues: 76.8514 Evaluate side-chains 303 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 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 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 LEU 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 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 500 GLU Chi-restraints excluded: chain B residue 546 SER 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 C residue 119 LEU Chi-restraints excluded: chain C residue 177 GLN 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 579 PHE Chi-restraints excluded: chain C residue 590 SER 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 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 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 557 CYS Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 656 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 284 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 190 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 78 optimal weight: 0.0070 chunk 45 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN ** A 134 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 = 0.3715 r_free = 0.3715 target = 0.107601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089892 restraints weight = 71099.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093019 restraints weight = 41365.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093354 restraints weight = 27671.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093788 restraints weight = 22208.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.093975 restraints weight = 20887.866| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23902 Z= 0.120 Angle : 0.668 10.983 32662 Z= 0.339 Chirality : 0.046 0.333 3862 Planarity : 0.004 0.056 4134 Dihedral : 5.914 50.465 3291 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.36 % Allowed : 21.79 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.15), residues: 3076 helix: 0.89 (0.15), residues: 1202 sheet: -1.76 (0.31), residues: 254 loop : -3.05 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 784 TYR 0.011 0.001 TYR A 668 PHE 0.012 0.001 PHE D 614 TRP 0.019 0.001 TRP D 285 HIS 0.002 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (23872) covalent geometry : angle 0.65733 / 0.34 (32590) SS BOND : bond 0.00358 / 0.26 ( 18) SS BOND : angle 1.35099 / 0.96 ( 36) hydrogen bonds : bond 0.04080 / 2.81 ( 914) hydrogen bonds : angle 4.88282 / 3.41 ( 2667) link_BETA1-4 : bond 0.00823 / 0.41 ( 2) link_BETA1-4 : angle 2.48335 / 1.35 ( 6) link_NAG-ASN : bond 0.00674 / 0.44 ( 10) link_NAG-ASN : angle 3.61690 / 2.87 ( 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 367 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 288 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8407 (ppp) cc_final: 0.6935 (mmt) REVERT: A 375 MET cc_start: 0.6838 (tpp) cc_final: 0.6274 (tpp) REVERT: A 579 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: A 806 MET cc_start: 0.9050 (tpp) cc_final: 0.8777 (mpp) REVERT: B 105 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6705 (mp10) REVERT: B 308 LEU cc_start: 0.6283 (mm) cc_final: 0.5741 (pp) REVERT: B 337 ARG cc_start: 0.8717 (tpt90) cc_final: 0.8140 (tpt90) REVERT: B 537 MET cc_start: 0.8282 (ttt) cc_final: 0.8071 (ttt) REVERT: B 562 MET cc_start: 0.8496 (tmm) cc_final: 0.8242 (tmm) REVERT: B 565 MET cc_start: 0.8300 (tpp) cc_final: 0.8096 (tpp) REVERT: B 568 ILE cc_start: 0.9170 (mt) cc_final: 0.8930 (mm) REVERT: B 656 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7709 (mm110) REVERT: B 818 MET cc_start: 0.8535 (mpp) cc_final: 0.8248 (mpp) REVERT: C 229 LEU cc_start: 0.8621 (tp) cc_final: 0.8414 (tp) REVERT: C 248 ASP cc_start: 0.7855 (m-30) cc_final: 0.7570 (m-30) REVERT: C 375 MET cc_start: 0.7223 (tpp) cc_final: 0.6974 (tpp) REVERT: C 579 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7055 (m-10) REVERT: C 733 GLU cc_start: 0.8031 (mp0) cc_final: 0.7718 (tp30) REVERT: C 783 MET cc_start: 0.7274 (mtm) cc_final: 0.6901 (mtm) REVERT: D 105 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: D 142 MET cc_start: 0.7657 (tpp) cc_final: 0.7413 (mmt) REVERT: D 308 LEU cc_start: 0.6618 (mm) cc_final: 0.5731 (pp) REVERT: D 337 ARG cc_start: 0.8835 (tpt90) cc_final: 0.8463 (tpt90) REVERT: D 565 MET cc_start: 0.7862 (tpp) cc_final: 0.7644 (tpp) REVERT: D 610 TRP cc_start: 0.9144 (OUTLIER) cc_final: 0.8937 (t-100) REVERT: D 656 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7780 (mm-40) REVERT: D 818 MET cc_start: 0.8403 (mpp) cc_final: 0.7717 (mtt) outliers start: 79 outliers final: 50 residues processed: 351 average time/residue: 0.1314 time to fit residues: 79.7029 Evaluate side-chains 318 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 268 TRP Chi-restraints excluded: chain A residue 366 ASP 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 663 ILE 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 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 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 119 LEU Chi-restraints excluded: chain C residue 177 GLN 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 497 VAL 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 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 105 GLN Chi-restraints excluded: chain D residue 126 ILE 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 557 CYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 612 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 218 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 57 optimal weight: 0.0870 chunk 204 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3719 r_free = 0.3719 target = 0.107883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.090133 restraints weight = 71439.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093569 restraints weight = 41268.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.093790 restraints weight = 26594.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.094122 restraints weight = 21644.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094314 restraints weight = 20580.505| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23902 Z= 0.120 Angle : 0.664 11.529 32662 Z= 0.334 Chirality : 0.046 0.268 3862 Planarity : 0.004 0.058 4134 Dihedral : 5.710 50.558 3290 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.96 % Allowed : 22.98 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.15), residues: 3076 helix: 0.96 (0.15), residues: 1204 sheet: -1.57 (0.30), residues: 272 loop : -2.95 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 692 TYR 0.011 0.001 TYR C 282 PHE 0.020 0.001 PHE B 575 TRP 0.021 0.001 TRP B 285 HIS 0.002 0.001 HIS C 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (23872) covalent geometry : angle 0.65412 / 0.33 (32590) SS BOND : bond 0.00330 / 0.22 ( 18) SS BOND : angle 1.25831 / 0.87 ( 36) hydrogen bonds : bond 0.03937 / 2.70 ( 914) hydrogen bonds : angle 4.78898 / 3.35 ( 2667) link_BETA1-4 : bond 0.00443 / 0.22 ( 2) link_BETA1-4 : angle 2.37801 / 1.30 ( 6) link_NAG-ASN : bond 0.00660 / 0.42 ( 10) link_NAG-ASN : angle 3.48205 / 2.76 ( 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 368 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 275 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8491 (ppp) cc_final: 0.7043 (mmt) REVERT: A 375 MET cc_start: 0.6673 (tpp) cc_final: 0.6218 (tpp) REVERT: A 579 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.6920 (m-10) REVERT: A 655 MET cc_start: 0.7675 (tmm) cc_final: 0.7246 (tmm) REVERT: A 723 MET cc_start: 0.9048 (mtm) cc_final: 0.8666 (ttm) REVERT: A 733 GLU cc_start: 0.8054 (mp0) cc_final: 0.7585 (tp30) REVERT: B 105 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: B 307 MET cc_start: 0.5136 (tpp) cc_final: 0.4127 (tpp) REVERT: B 308 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6081 (pp) REVERT: B 337 ARG cc_start: 0.8656 (tpt90) cc_final: 0.8218 (tpt90) REVERT: B 568 ILE cc_start: 0.9179 (mt) cc_final: 0.8915 (mm) REVERT: B 656 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7906 (mm-40) REVERT: B 800 ILE cc_start: 0.8418 (pt) cc_final: 0.8175 (tp) REVERT: B 818 MET cc_start: 0.8455 (mpp) cc_final: 0.8190 (mpp) REVERT: C 248 ASP cc_start: 0.7742 (m-30) cc_final: 0.7399 (m-30) REVERT: C 375 MET cc_start: 0.7361 (tpp) cc_final: 0.6957 (tpp) REVERT: C 579 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7093 (m-10) REVERT: C 733 GLU cc_start: 0.8063 (mp0) cc_final: 0.7622 (tp30) REVERT: C 783 MET cc_start: 0.7230 (mtm) cc_final: 0.6827 (mtm) REVERT: D 105 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: D 142 MET cc_start: 0.7648 (tpp) cc_final: 0.7426 (mmt) REVERT: D 308 LEU cc_start: 0.6397 (mm) cc_final: 0.5616 (tt) REVERT: D 337 ARG cc_start: 0.8656 (tpt90) cc_final: 0.8203 (tpt90) REVERT: D 563 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8038 (m-80) outliers start: 93 outliers final: 62 residues processed: 345 average time/residue: 0.1253 time to fit residues: 74.6950 Evaluate side-chains 328 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 366 ASP 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 734 SER 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 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 119 LEU Chi-restraints excluded: chain C residue 177 GLN 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 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 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 SER 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 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 390 VAL Chi-restraints excluded: chain D residue 422 VAL 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 612 LEU Chi-restraints excluded: chain D residue 660 VAL 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: 0.7980 chunk 71 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.107504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089720 restraints weight = 71420.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.093270 restraints weight = 41529.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.093351 restraints weight = 27257.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.093481 restraints weight = 23017.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093946 restraints weight = 21387.536| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23902 Z= 0.132 Angle : 0.673 14.185 32662 Z= 0.337 Chirality : 0.045 0.256 3862 Planarity : 0.004 0.061 4134 Dihedral : 5.624 50.550 3290 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 3.83 % Allowed : 22.72 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.15), residues: 3076 helix: 0.96 (0.15), residues: 1212 sheet: -1.67 (0.30), residues: 278 loop : -2.85 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 375 TYR 0.007 0.001 TYR A 668 PHE 0.022 0.001 PHE D 575 TRP 0.024 0.001 TRP D 285 HIS 0.004 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (23872) covalent geometry : angle 0.66318 / 0.33 (32590) SS BOND : bond 0.00284 / 0.19 ( 18) SS BOND : angle 1.47493 / 0.94 ( 36) hydrogen bonds : bond 0.04040 / 2.77 ( 914) hydrogen bonds : angle 4.79404 / 3.35 ( 2667) link_BETA1-4 : bond 0.00577 / 0.29 ( 2) link_BETA1-4 : angle 2.26044 / 1.23 ( 6) link_NAG-ASN : bond 0.00617 / 0.39 ( 10) link_NAG-ASN : angle 3.40460 / 2.70 ( 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 366 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 276 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8472 (ppp) cc_final: 0.7060 (mmt) REVERT: A 375 MET cc_start: 0.6703 (tpp) cc_final: 0.6232 (tpp) REVERT: A 579 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.6963 (m-10) REVERT: A 733 GLU cc_start: 0.8068 (mp0) cc_final: 0.7745 (tp30) REVERT: B 37 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4807 (mt) REVERT: B 105 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: B 307 MET cc_start: 0.5215 (tpp) cc_final: 0.4401 (tpp) REVERT: B 308 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6086 (pp) REVERT: B 337 ARG cc_start: 0.8725 (tpt90) cc_final: 0.8301 (tpt90) REVERT: B 568 ILE cc_start: 0.9185 (mt) cc_final: 0.8927 (mm) REVERT: B 818 MET cc_start: 0.8497 (mpp) cc_final: 0.8201 (mpp) REVERT: C 248 ASP cc_start: 0.7707 (m-30) cc_final: 0.7383 (m-30) REVERT: C 579 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7145 (m-10) REVERT: C 733 GLU cc_start: 0.8012 (mp0) cc_final: 0.7714 (tp30) REVERT: C 783 MET cc_start: 0.7118 (mtm) cc_final: 0.6793 (mtm) REVERT: D 105 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7168 (pm20) REVERT: D 142 MET cc_start: 0.7647 (tpp) cc_final: 0.7426 (mmt) REVERT: D 143 PHE cc_start: 0.8323 (t80) cc_final: 0.7371 (t80) REVERT: D 308 LEU cc_start: 0.6406 (mm) cc_final: 0.5651 (tt) REVERT: D 337 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8306 (tpt90) REVERT: D 656 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8002 (mm-40) outliers start: 90 outliers final: 68 residues processed: 342 average time/residue: 0.1315 time to fit residues: 77.1735 Evaluate side-chains 342 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain A residue 366 ASP 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 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 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 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 655 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 119 LEU 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 477 TYR 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 656 VAL 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 105 GLN Chi-restraints excluded: chain D residue 126 ILE 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 422 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 VAL 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 612 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 242 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 78 optimal weight: 0.0020 chunk 188 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** 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 = 0.3702 r_free = 0.3702 target = 0.106900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089068 restraints weight = 71427.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092569 restraints weight = 41536.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092715 restraints weight = 26668.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093019 restraints weight = 21849.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093179 restraints weight = 20780.840| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23902 Z= 0.145 Angle : 0.685 17.209 32662 Z= 0.342 Chirality : 0.046 0.257 3862 Planarity : 0.004 0.059 4134 Dihedral : 5.652 50.343 3290 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 4.00 % Allowed : 23.06 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 3076 helix: 1.04 (0.16), residues: 1206 sheet: -1.64 (0.29), residues: 294 loop : -2.73 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 375 TYR 0.010 0.001 TYR C 282 PHE 0.019 0.001 PHE B 575 TRP 0.029 0.001 TRP D 285 HIS 0.006 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (23872) covalent geometry : angle 0.67545 / 0.34 (32590) SS BOND : bond 0.00287 / 0.18 ( 18) SS BOND : angle 1.43149 / 0.92 ( 36) hydrogen bonds : bond 0.04153 / 2.84 ( 914) hydrogen bonds : angle 4.80262 / 3.35 ( 2667) link_BETA1-4 : bond 0.00508 / 0.25 ( 2) link_BETA1-4 : angle 2.24720 / 1.23 ( 6) link_NAG-ASN : bond 0.00611 / 0.38 ( 10) link_NAG-ASN : angle 3.34571 / 2.65 ( 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 369 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 275 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.8715 (mmt) cc_final: 0.8340 (mpp) REVERT: A 347 MET cc_start: 0.8443 (ppp) cc_final: 0.7077 (mmt) REVERT: A 375 MET cc_start: 0.6517 (tpp) cc_final: 0.6098 (tpp) REVERT: A 579 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.6978 (m-10) REVERT: B 37 ILE cc_start: 0.5519 (OUTLIER) cc_final: 0.4787 (mt) REVERT: B 105 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6644 (pm20) REVERT: B 143 PHE cc_start: 0.7916 (t80) cc_final: 0.7221 (t80) REVERT: B 307 MET cc_start: 0.5186 (tpp) cc_final: 0.4518 (tpp) REVERT: B 308 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6085 (pp) REVERT: B 337 ARG cc_start: 0.8684 (tpt90) cc_final: 0.8334 (tpt90) REVERT: B 568 ILE cc_start: 0.9201 (mt) cc_final: 0.8985 (mm) REVERT: B 656 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7819 (mm-40) REVERT: B 818 MET cc_start: 0.8517 (mpp) cc_final: 0.8207 (mpp) REVERT: C 248 ASP cc_start: 0.7725 (m-30) cc_final: 0.7415 (m-30) REVERT: C 579 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7084 (m-10) REVERT: C 733 GLU cc_start: 0.8091 (mp0) cc_final: 0.7615 (tp30) REVERT: C 783 MET cc_start: 0.7171 (mtm) cc_final: 0.6812 (mtm) REVERT: D 105 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: D 142 MET cc_start: 0.7651 (tpp) cc_final: 0.7438 (mmt) REVERT: D 143 PHE cc_start: 0.8309 (t80) cc_final: 0.7378 (t80) REVERT: D 308 LEU cc_start: 0.6561 (mm) cc_final: 0.5821 (tt) REVERT: D 337 ARG cc_start: 0.8744 (tpt90) cc_final: 0.8288 (tpt90) REVERT: D 656 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7981 (mm-40) outliers start: 94 outliers final: 73 residues processed: 350 average time/residue: 0.1308 time to fit residues: 78.8745 Evaluate side-chains 351 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 270 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 270 VAL 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 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 37 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 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 422 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 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 119 LEU 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 477 TYR 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 656 VAL 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 161 MET 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 510 VAL Chi-restraints excluded: chain D residue 523 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 626 THR Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 829 MET 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: 2.9990 chunk 224 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 271 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 266 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 303 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 HIS A 171 HIS ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 171 HIS ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.109271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091689 restraints weight = 70738.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094867 restraints weight = 41569.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095069 restraints weight = 29168.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095328 restraints weight = 23413.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.095860 restraints weight = 21785.079| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23902 Z= 0.114 Angle : 0.673 17.605 32662 Z= 0.333 Chirality : 0.045 0.263 3862 Planarity : 0.004 0.061 4134 Dihedral : 5.407 50.743 3290 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.23 % Allowed : 23.45 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.15), residues: 3076 helix: 1.12 (0.15), residues: 1208 sheet: -1.68 (0.29), residues: 302 loop : -2.61 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 337 TYR 0.009 0.001 TYR A 668 PHE 0.011 0.001 PHE A 42 TRP 0.025 0.001 TRP D 285 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (23872) covalent geometry : angle 0.66441 / 0.33 (32590) SS BOND : bond 0.00282 / 0.20 ( 18) SS BOND : angle 1.28681 / 0.88 ( 36) hydrogen bonds : bond 0.03682 / 2.53 ( 914) hydrogen bonds : angle 4.63926 / 3.24 ( 2667) link_BETA1-4 : bond 0.00627 / 0.31 ( 2) link_BETA1-4 : angle 2.02025 / 1.10 ( 6) link_NAG-ASN : bond 0.00682 / 0.44 ( 10) link_NAG-ASN : angle 3.18090 / 2.53 ( 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 370 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 294 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ILE cc_start: 0.7919 (pt) cc_final: 0.7615 (tp) REVERT: A 282 TYR cc_start: 0.7892 (m-80) cc_final: 0.7633 (m-10) REVERT: A 347 MET cc_start: 0.8441 (ppp) cc_final: 0.7065 (mmt) REVERT: A 375 MET cc_start: 0.6637 (tpp) cc_final: 0.6166 (tpp) REVERT: A 579 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.6974 (m-10) REVERT: A 733 GLU cc_start: 0.8131 (mp0) cc_final: 0.7649 (tp30) REVERT: B 37 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4631 (mt) REVERT: B 105 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: B 142 MET cc_start: 0.7653 (mmm) cc_final: 0.5932 (ttm) REVERT: B 143 PHE cc_start: 0.7740 (t80) cc_final: 0.7262 (t80) REVERT: B 307 MET cc_start: 0.4967 (tpp) cc_final: 0.4466 (tpp) REVERT: B 308 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6037 (pp) REVERT: B 337 ARG cc_start: 0.8746 (tpt90) cc_final: 0.8429 (tpt90) REVERT: B 568 ILE cc_start: 0.9184 (mt) cc_final: 0.8966 (mm) REVERT: B 656 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7774 (mm-40) REVERT: B 727 ASP cc_start: 0.8260 (p0) cc_final: 0.7686 (p0) REVERT: B 818 MET cc_start: 0.8406 (mpp) cc_final: 0.8108 (mpp) REVERT: C 248 ASP cc_start: 0.7779 (m-30) cc_final: 0.7553 (m-30) REVERT: C 282 TYR cc_start: 0.8017 (m-80) cc_final: 0.7736 (m-10) REVERT: C 579 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.6864 (m-10) REVERT: C 655 MET cc_start: 0.7489 (ttp) cc_final: 0.7079 (ttp) REVERT: C 723 MET cc_start: 0.8976 (mtm) cc_final: 0.8651 (ttm) REVERT: C 733 GLU cc_start: 0.8043 (mp0) cc_final: 0.7631 (tp30) REVERT: C 783 MET cc_start: 0.7186 (mtm) cc_final: 0.6873 (mtm) REVERT: D 105 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: D 142 MET cc_start: 0.7610 (tpp) cc_final: 0.7400 (mmt) REVERT: D 308 LEU cc_start: 0.6579 (mm) cc_final: 0.6080 (tt) REVERT: D 337 ARG cc_start: 0.8663 (tpt90) cc_final: 0.8339 (tpt90) REVERT: D 656 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7959 (mm-40) outliers start: 76 outliers final: 60 residues processed: 353 average time/residue: 0.1237 time to fit residues: 75.4933 Evaluate side-chains 344 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 270 VAL 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 686 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 SER 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 37 ILE 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 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 422 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 119 LEU 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 477 TYR 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 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 275 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 138 optimal weight: 0.0970 chunk 239 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.3741 r_free = 0.3741 target = 0.109158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091355 restraints weight = 70547.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094967 restraints weight = 40672.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.095130 restraints weight = 25974.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095271 restraints weight = 22149.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.095850 restraints weight = 20612.971| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23902 Z= 0.120 Angle : 0.699 18.035 32662 Z= 0.339 Chirality : 0.045 0.262 3862 Planarity : 0.004 0.061 4134 Dihedral : 5.360 50.630 3290 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 3.06 % Allowed : 24.21 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.15), residues: 3076 helix: 1.16 (0.16), residues: 1208 sheet: -1.59 (0.29), residues: 296 loop : -2.53 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.008 0.001 TYR A 668 PHE 0.026 0.001 PHE B 575 TRP 0.035 0.001 TRP D 285 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (23872) covalent geometry : angle 0.69139 / 0.34 (32590) SS BOND : bond 0.00276 / 0.19 ( 18) SS BOND : angle 1.35865 / 0.94 ( 36) hydrogen bonds : bond 0.03733 / 2.57 ( 914) hydrogen bonds : angle 4.66018 / 3.25 ( 2667) link_BETA1-4 : bond 0.00603 / 0.30 ( 2) link_BETA1-4 : angle 2.01228 / 1.09 ( 6) link_NAG-ASN : bond 0.00650 / 0.41 ( 10) link_NAG-ASN : angle 3.14551 / 2.50 ( 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 354 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 282 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 282 TYR cc_start: 0.7865 (m-80) cc_final: 0.7611 (m-10) REVERT: A 347 MET cc_start: 0.8478 (ppp) cc_final: 0.7062 (mmt) REVERT: A 375 MET cc_start: 0.6562 (tpp) cc_final: 0.6089 (tpp) REVERT: A 576 MET cc_start: 0.8066 (mmm) cc_final: 0.7656 (mmp) REVERT: A 579 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.6821 (m-10) REVERT: A 733 GLU cc_start: 0.8171 (mp0) cc_final: 0.7648 (tp30) REVERT: B 37 ILE cc_start: 0.5435 (OUTLIER) cc_final: 0.4753 (mt) REVERT: B 105 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: B 143 PHE cc_start: 0.7944 (t80) cc_final: 0.7479 (t80) REVERT: B 308 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6095 (pp) REVERT: B 337 ARG cc_start: 0.8770 (tpt90) cc_final: 0.8437 (tpt90) REVERT: B 568 ILE cc_start: 0.9199 (mt) cc_final: 0.8997 (mm) REVERT: B 656 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7979 (mm-40) REVERT: B 818 MET cc_start: 0.8480 (mpp) cc_final: 0.8171 (mpp) REVERT: C 155 MET cc_start: 0.8429 (mpp) cc_final: 0.8043 (mpp) REVERT: C 248 ASP cc_start: 0.7832 (m-30) cc_final: 0.7576 (m-30) REVERT: C 579 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.6803 (m-10) REVERT: C 733 GLU cc_start: 0.8087 (mp0) cc_final: 0.7643 (tp30) REVERT: C 783 MET cc_start: 0.7201 (mtm) cc_final: 0.6919 (mtm) REVERT: D 105 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: D 143 PHE cc_start: 0.8112 (t80) cc_final: 0.7285 (t80) REVERT: D 308 LEU cc_start: 0.6641 (mm) cc_final: 0.6177 (tt) REVERT: D 337 ARG cc_start: 0.8725 (tpt90) cc_final: 0.8285 (tpt90) REVERT: D 656 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7863 (mm-40) outliers start: 72 outliers final: 62 residues processed: 338 average time/residue: 0.1324 time to fit residues: 77.1936 Evaluate side-chains 346 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 276 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 573 ASP Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER 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 B residue 37 ILE 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 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 422 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 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 119 LEU 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 477 TYR 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 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 734 SER 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 275 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 557 CYS 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 289 optimal weight: 0.9980 chunk 292 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 271 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 177 GLN ** A 474 GLN ** 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 = 0.3715 r_free = 0.3715 target = 0.107684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089581 restraints weight = 70124.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093585 restraints weight = 39091.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.093634 restraints weight = 23454.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093755 restraints weight = 20740.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.093999 restraints weight = 19167.755| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23902 Z= 0.140 Angle : 0.705 17.813 32662 Z= 0.345 Chirality : 0.046 0.256 3862 Planarity : 0.004 0.060 4134 Dihedral : 5.391 51.184 3290 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 3.32 % Allowed : 24.13 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3076 helix: 1.15 (0.16), residues: 1208 sheet: -1.54 (0.30), residues: 284 loop : -2.51 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 337 TYR 0.011 0.001 TYR C 282 PHE 0.016 0.001 PHE B 653 TRP 0.034 0.001 TRP C 336 HIS 0.002 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (23872) covalent geometry : angle 0.69684 / 0.34 (32590) SS BOND : bond 0.00276 / 0.18 ( 18) SS BOND : angle 1.37270 / 0.94 ( 36) hydrogen bonds : bond 0.03949 / 2.71 ( 914) hydrogen bonds : angle 4.70250 / 3.28 ( 2667) link_BETA1-4 : bond 0.00476 / 0.24 ( 2) link_BETA1-4 : angle 2.06581 / 1.13 ( 6) link_NAG-ASN : bond 0.00595 / 0.38 ( 10) link_NAG-ASN : angle 3.15284 / 2.50 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.60 seconds wall clock time: 59 minutes 17.18 seconds (3557.18 seconds total)