Starting phenix.real_space_refine on Fri Jun 20 01:31:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6whu_21676/06_2025/6whu_21676.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whu_21676/06_2025/6whu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6whu_21676/06_2025/6whu_21676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whu_21676/06_2025/6whu_21676.map" model { file = "/net/cci-nas-00/data/ceres_data/6whu_21676/06_2025/6whu_21676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whu_21676/06_2025/6whu_21676.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 25} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 11} 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: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 25} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 213 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 14.87, per 1000 atoms: 0.64 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: 6.19 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 2.87 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: 9.63 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3918 1.31 - 1.44: 6372 1.44 - 1.57: 13338 1.57 - 1.70: 4 1.70 - 1.83: 240 Bond restraints: 23872 Sorted by residual: bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.851 1.591 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.851 1.591 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" O3 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.629 1.472 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" O3 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.629 1.474 0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 1.347 1.476 -0.129 2.00e-02 2.50e+03 4.15e+01 ... (remaining 23867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 31607 2.42 - 4.85: 843 4.85 - 7.27: 126 7.27 - 9.69: 12 9.69 - 12.12: 2 Bond angle restraints: 32590 Sorted by residual: angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.20 108.26 4.94 9.60e-01 1.09e+00 2.65e+01 angle pdb=" N VAL A 225 " pdb=" CA VAL A 225 " pdb=" C VAL A 225 " ideal model delta sigma weight residual 113.20 108.28 4.92 9.60e-01 1.09e+00 2.62e+01 angle pdb=" N HIS B 802 " pdb=" CA HIS B 802 " pdb=" C HIS B 802 " ideal model delta sigma weight residual 113.88 108.32 5.56 1.23e+00 6.61e-01 2.04e+01 angle pdb=" N HIS D 802 " pdb=" CA HIS D 802 " pdb=" C HIS D 802 " ideal model delta sigma weight residual 113.88 108.41 5.47 1.23e+00 6.61e-01 1.98e+01 angle pdb=" C GLN C 378 " pdb=" N ASN C 379 " pdb=" CA ASN C 379 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 ... (remaining 32585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 13163 23.29 - 46.58: 844 46.58 - 69.86: 133 69.86 - 93.15: 32 93.15 - 116.44: 14 Dihedral angle restraints: 14186 sinusoidal: 5168 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS D 746 " pdb=" SG CYS D 746 " pdb=" SG CYS D 801 " pdb=" CB CYS D 801 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS B 746 " pdb=" SG CYS B 746 " pdb=" SG CYS B 801 " pdb=" CB CYS B 801 " ideal model delta sinusoidal sigma weight residual -86.00 -155.88 69.88 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS A 441 " pdb=" SG CYS A 441 " pdb=" SG CYS A 475 " pdb=" CB CYS A 475 " ideal model delta sinusoidal sigma weight residual 93.00 33.79 59.21 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 14183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3756 0.119 - 0.238: 100 0.238 - 0.357: 2 0.357 - 0.476: 2 0.476 - 0.595: 2 Chirality restraints: 3862 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" CG LEU A 119 " pdb=" CB LEU A 119 " pdb=" CD1 LEU A 119 " pdb=" CD2 LEU A 119 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.59 2.00e-01 2.50e+01 8.85e+00 ... (remaining 3859 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 128 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY B 128 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY B 128 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 129 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 128 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLY D 128 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY D 128 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 700 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C ALA B 700 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 700 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 701 " -0.013 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 702 2.66 - 3.22: 25378 3.22 - 3.78: 34842 3.78 - 4.34: 43763 4.34 - 4.90: 68264 Nonbonded interactions: 172949 Sorted by model distance: nonbonded pdb=" NH2 ARG A 233 " pdb=" O MET A 258 " model vdw 2.095 3.120 nonbonded pdb=" NH2 ARG C 233 " pdb=" O MET C 258 " model vdw 2.105 3.120 nonbonded pdb=" O MET B 829 " pdb=" OG SER B 832 " model vdw 2.137 3.040 nonbonded pdb=" O MET D 829 " pdb=" OG SER D 832 " model vdw 2.138 3.040 nonbonded pdb=" O LYS B 380 " pdb=" OG SER B 383 " model vdw 2.166 3.040 ... (remaining 172944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 1.040 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: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 56.150 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.260 23902 Z= 0.435 Angle : 1.011 36.585 32662 Z= 0.534 Chirality : 0.054 0.595 3862 Planarity : 0.005 0.049 4134 Dihedral : 16.309 116.438 8308 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.032 0.002 TRP A 268 HIS 0.009 0.002 HIS A 801 PHE 0.020 0.002 PHE B 99 TYR 0.023 0.002 TYR C 816 ARG 0.005 0.001 ARG D 375 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 10) link_NAG-ASN : angle 4.50847 ( 30) link_BETA1-4 : bond 0.06412 ( 2) link_BETA1-4 : angle 23.61657 ( 6) hydrogen bonds : bond 0.18535 ( 914) hydrogen bonds : angle 7.86094 ( 2667) SS BOND : bond 0.00713 ( 18) SS BOND : angle 2.23627 ( 36) covalent geometry : bond 0.00910 (23872) covalent geometry : angle 0.94764 (32590) *********************** 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 : 3.062 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: 0.7126 (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: 0.8759 (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: 0.3787 time to fit residues: 211.3848 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 : 3.485 ------------------------------------------------------------------------------- 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 261 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 158 optimal weight: 40.0000 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 281 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 146 HIS A 161 ASN A 291 GLN A 707 GLN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 745 ASN A 763 GLN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.103654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086473 restraints weight = 69791.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.087318 restraints weight = 41070.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088270 restraints weight = 33004.491| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23902 Z= 0.177 Angle : 0.769 12.206 32662 Z= 0.396 Chirality : 0.050 0.490 3862 Planarity : 0.005 0.060 4134 Dihedral : 10.546 107.273 3580 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 2.47 % Allowed : 16.47 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.14), residues: 3076 helix: -0.35 (0.14), residues: 1208 sheet: -2.71 (0.24), residues: 350 loop : -3.64 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 197 HIS 0.004 0.001 HIS C 171 PHE 0.018 0.002 PHE B 614 TYR 0.013 0.001 TYR D 282 ARG 0.005 0.001 ARG C 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 10) link_NAG-ASN : angle 4.45697 ( 30) link_BETA1-4 : bond 0.00387 ( 2) link_BETA1-4 : angle 4.97963 ( 6) hydrogen bonds : bond 0.05837 ( 914) hydrogen bonds : angle 5.72830 ( 2667) SS BOND : bond 0.00493 ( 18) SS BOND : angle 1.62955 ( 36) covalent geometry : bond 0.00398 (23872) covalent geometry : angle 0.75264 (32590) *********************** 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 342 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8424 (ppp) cc_final: 0.6960 (mmt) REVERT: A 375 MET cc_start: 0.6922 (tpp) cc_final: 0.6627 (tpp) REVERT: A 385 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8016 (t) REVERT: A 597 MET cc_start: 0.8474 (mmm) cc_final: 0.8192 (ttt) REVERT: A 640 ILE cc_start: 0.9069 (tp) cc_final: 0.8774 (tt) REVERT: A 662 MET cc_start: 0.9495 (tmm) cc_final: 0.9199 (tmm) REVERT: B 73 MET cc_start: 0.6735 (mtt) cc_final: 0.6527 (ptp) REVERT: B 105 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: B 308 LEU cc_start: 0.6908 (mm) cc_final: 0.5704 (pp) REVERT: B 786 ASP cc_start: 0.8334 (t0) cc_final: 0.8086 (t0) REVERT: B 818 MET cc_start: 0.8713 (mpp) cc_final: 0.8119 (mtm) REVERT: C 248 ASP cc_start: 0.8039 (m-30) cc_final: 0.7784 (m-30) REVERT: C 491 MET cc_start: 0.8385 (mtp) cc_final: 0.8156 (mtp) REVERT: C 597 MET cc_start: 0.8432 (mmm) cc_final: 0.8120 (ttt) REVERT: C 662 MET cc_start: 0.9489 (tmm) cc_final: 0.9268 (tmm) REVERT: D 73 MET cc_start: 0.6998 (mtt) cc_final: 0.6738 (mtt) REVERT: D 101 ASP cc_start: 0.8934 (t0) cc_final: 0.8718 (t0) REVERT: D 105 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: D 142 MET cc_start: 0.7727 (tpp) cc_final: 0.7427 (mmt) REVERT: D 386 MET cc_start: 0.8409 (mmm) cc_final: 0.8079 (mmm) REVERT: D 818 MET cc_start: 0.8636 (mpp) cc_final: 0.7885 (mtm) outliers start: 58 outliers final: 33 residues processed: 332 average time/residue: 0.2727 time to fit residues: 156.8474 Evaluate side-chains 276 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 2.732 ------------------------------------------------------------------------------- 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 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 105 GLN 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 129 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 257 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 HIS ** C 726 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 = 0.3710 r_free = 0.3710 target = 0.107044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.089483 restraints weight = 71023.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.092990 restraints weight = 41244.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093201 restraints weight = 25888.698| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2285 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= 0.126 Angle : 0.700 12.026 32662 Z= 0.354 Chirality : 0.048 0.565 3862 Planarity : 0.004 0.055 4134 Dihedral : 9.187 93.431 3576 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 2.89 % Allowed : 18.30 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.15), residues: 3076 helix: 0.43 (0.15), residues: 1214 sheet: -2.26 (0.27), residues: 322 loop : -3.31 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 197 HIS 0.003 0.001 HIS D 127 PHE 0.015 0.001 PHE D 194 TYR 0.012 0.001 TYR C 668 ARG 0.003 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 10) link_NAG-ASN : angle 4.25796 ( 30) link_BETA1-4 : bond 0.01019 ( 2) link_BETA1-4 : angle 3.99260 ( 6) hydrogen bonds : bond 0.04544 ( 914) hydrogen bonds : angle 5.15649 ( 2667) SS BOND : bond 0.00333 ( 18) SS BOND : angle 1.56912 ( 36) covalent geometry : bond 0.00269 (23872) covalent geometry : angle 0.68469 (32590) *********************** 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 346 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7711 (mmm) cc_final: 0.7358 (mmp) REVERT: A 347 MET cc_start: 0.8448 (ppp) cc_final: 0.6955 (mmt) REVERT: A 375 MET cc_start: 0.7142 (tpp) cc_final: 0.6743 (tpp) REVERT: A 385 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7800 (t) REVERT: A 597 MET cc_start: 0.8358 (mmm) cc_final: 0.7972 (ttt) REVERT: A 640 ILE cc_start: 0.9024 (tp) cc_final: 0.8749 (tt) REVERT: A 662 MET cc_start: 0.9438 (tmm) cc_final: 0.9206 (tmm) REVERT: A 783 MET cc_start: 0.7218 (mtm) cc_final: 0.7016 (mtm) REVERT: A 806 MET cc_start: 0.9061 (tpp) cc_final: 0.8388 (mpp) REVERT: B 308 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.5874 (pp) REVERT: B 788 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8018 (mm-30) REVERT: B 818 MET cc_start: 0.8675 (mpp) cc_final: 0.7962 (mtt) REVERT: C 248 ASP cc_start: 0.7874 (m-30) cc_final: 0.7577 (m-30) REVERT: C 385 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7874 (t) REVERT: C 579 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.6902 (m-10) REVERT: C 597 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8093 (ttt) REVERT: C 723 MET cc_start: 0.9032 (mtm) cc_final: 0.8635 (ttm) REVERT: C 733 GLU cc_start: 0.8066 (mp0) cc_final: 0.7757 (tp30) REVERT: C 783 MET cc_start: 0.7438 (mtm) cc_final: 0.7079 (mtm) REVERT: D 142 MET cc_start: 0.7714 (tpp) cc_final: 0.7427 (mmt) REVERT: D 308 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.5629 (pp) REVERT: D 818 MET cc_start: 0.8462 (mpp) cc_final: 0.7862 (mtt) outliers start: 68 outliers final: 38 residues processed: 325 average time/residue: 0.2701 time to fit residues: 150.2061 Evaluate side-chains 296 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 477 TYR 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 841 VAL Chi-restraints excluded: chain B residue 35 ILE 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 388 TYR 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 C residue 177 GLN Chi-restraints excluded: chain C residue 268 TRP Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 500 GLU 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 563 PHE Chi-restraints excluded: chain D residue 612 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 83 optimal weight: 8.9990 chunk 263 optimal weight: 0.0000 chunk 147 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 307 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 249 optimal weight: 0.9980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS C 134 HIS C 726 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.108280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.090543 restraints weight = 71930.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093936 restraints weight = 41747.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094232 restraints weight = 26593.860| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2679 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= 0.117 Angle : 0.662 11.656 32662 Z= 0.333 Chirality : 0.046 0.631 3862 Planarity : 0.004 0.056 4134 Dihedral : 8.213 72.739 3576 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 3.02 % Allowed : 19.45 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.15), residues: 3076 helix: 0.77 (0.15), residues: 1214 sheet: -2.10 (0.29), residues: 294 loop : -3.04 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 285 HIS 0.003 0.001 HIS D 127 PHE 0.012 0.001 PHE D 614 TYR 0.011 0.001 TYR C 282 ARG 0.002 0.000 ARG C 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 10) link_NAG-ASN : angle 4.01968 ( 30) link_BETA1-4 : bond 0.00684 ( 2) link_BETA1-4 : angle 3.41189 ( 6) hydrogen bonds : bond 0.04033 ( 914) hydrogen bonds : angle 4.86295 ( 2667) SS BOND : bond 0.00357 ( 18) SS BOND : angle 1.40844 ( 36) covalent geometry : bond 0.00250 (23872) covalent geometry : angle 0.64814 (32590) *********************** 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 352 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 281 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 TYR cc_start: 0.7877 (m-80) cc_final: 0.7630 (m-10) REVERT: A 375 MET cc_start: 0.6973 (tpp) cc_final: 0.6564 (tpp) REVERT: A 385 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7737 (t) REVERT: A 579 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: A 597 MET cc_start: 0.8281 (mmm) cc_final: 0.7935 (ttt) REVERT: A 640 ILE cc_start: 0.9032 (tp) cc_final: 0.8738 (tt) REVERT: A 733 GLU cc_start: 0.8083 (mp0) cc_final: 0.7615 (tp30) REVERT: A 806 MET cc_start: 0.9124 (tpp) cc_final: 0.8559 (mpp) REVERT: B 105 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: B 205 LEU cc_start: 0.8750 (mm) cc_final: 0.8191 (tp) REVERT: B 308 LEU cc_start: 0.6395 (mm) cc_final: 0.5891 (pp) REVERT: B 551 LEU cc_start: 0.9174 (mt) cc_final: 0.8798 (tt) REVERT: B 656 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7740 (mm110) REVERT: B 818 MET cc_start: 0.8488 (mpp) cc_final: 0.8217 (mpp) REVERT: C 248 ASP cc_start: 0.7886 (m-30) cc_final: 0.7557 (m-30) REVERT: C 385 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7873 (t) REVERT: C 579 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.6781 (m-10) REVERT: C 597 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8089 (ttt) REVERT: C 733 GLU cc_start: 0.8031 (mp0) cc_final: 0.7641 (tp30) REVERT: C 783 MET cc_start: 0.7319 (mtm) cc_final: 0.6921 (mtm) REVERT: D 73 MET cc_start: 0.6564 (mtt) cc_final: 0.6281 (ptp) REVERT: D 105 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: D 142 MET cc_start: 0.7678 (tpp) cc_final: 0.7414 (mmt) REVERT: D 308 LEU cc_start: 0.6633 (mm) cc_final: 0.5714 (pp) REVERT: D 337 ARG cc_start: 0.8771 (tpt90) cc_final: 0.8381 (tpt90) REVERT: D 656 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7831 (mm110) REVERT: D 818 MET cc_start: 0.8307 (mpp) cc_final: 0.7652 (mtt) outliers start: 71 outliers final: 43 residues processed: 335 average time/residue: 0.2744 time to fit residues: 156.6596 Evaluate side-chains 311 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 477 TYR 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 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 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 837 ILE 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 385 VAL Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 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 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 510 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 656 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 231 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 chunk 75 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 498 HIS C 498 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.106555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088829 restraints weight = 71596.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092290 restraints weight = 41994.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092469 restraints weight = 26956.540| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23902 Z= 0.146 Angle : 0.678 11.393 32662 Z= 0.341 Chirality : 0.048 0.929 3862 Planarity : 0.004 0.058 4134 Dihedral : 7.323 56.552 3574 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 4.00 % Allowed : 20.17 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 3076 helix: 0.86 (0.15), residues: 1216 sheet: -1.93 (0.30), residues: 258 loop : -2.94 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 285 HIS 0.003 0.001 HIS A 801 PHE 0.022 0.001 PHE D 575 TYR 0.010 0.001 TYR B 282 ARG 0.002 0.000 ARG A 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 10) link_NAG-ASN : angle 4.19288 ( 30) link_BETA1-4 : bond 0.00407 ( 2) link_BETA1-4 : angle 3.25562 ( 6) hydrogen bonds : bond 0.04249 ( 914) hydrogen bonds : angle 4.85001 ( 2667) SS BOND : bond 0.00362 ( 18) SS BOND : angle 1.33720 ( 36) covalent geometry : bond 0.00332 (23872) covalent geometry : angle 0.66393 (32590) *********************** 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 360 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 266 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.8351 (ppp) cc_final: 0.6798 (mmt) REVERT: A 375 MET cc_start: 0.6973 (tpp) cc_final: 0.6539 (tpp) REVERT: A 385 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7908 (t) REVERT: A 579 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7156 (m-10) REVERT: A 597 MET cc_start: 0.8207 (mmm) cc_final: 0.7910 (ttt) REVERT: A 723 MET cc_start: 0.9087 (mtm) cc_final: 0.8666 (ttm) REVERT: A 806 MET cc_start: 0.9075 (tpp) cc_final: 0.8738 (mpp) REVERT: B 105 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6841 (pm20) REVERT: B 308 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5788 (pp) REVERT: B 551 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8872 (tt) REVERT: B 656 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: B 818 MET cc_start: 0.8493 (mpp) cc_final: 0.8219 (mpp) REVERT: C 248 ASP cc_start: 0.7730 (m-30) cc_final: 0.7432 (m-30) REVERT: C 579 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7075 (m-10) REVERT: C 597 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8077 (ttt) REVERT: C 733 GLU cc_start: 0.8031 (mp0) cc_final: 0.7775 (tp30) REVERT: C 783 MET cc_start: 0.7283 (mtm) cc_final: 0.6930 (mtm) REVERT: D 73 MET cc_start: 0.6700 (mtt) cc_final: 0.6421 (ptp) REVERT: D 105 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: D 142 MET cc_start: 0.7679 (tpp) cc_final: 0.7403 (mmt) REVERT: D 308 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.5757 (pp) REVERT: D 337 ARG cc_start: 0.8838 (tpt90) cc_final: 0.8513 (tpt90) REVERT: D 656 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7886 (mm-40) REVERT: D 793 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8283 (mt-10) outliers start: 94 outliers final: 60 residues processed: 337 average time/residue: 0.2674 time to fit residues: 154.8992 Evaluate side-chains 321 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 250 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 558 VAL 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 829 MET Chi-restraints excluded: chain B residue 837 ILE 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 579 PHE Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 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 308 LEU 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 656 GLN Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 293 optimal weight: 0.0470 chunk 154 optimal weight: 3.9990 chunk 156 optimal weight: 30.0000 chunk 60 optimal weight: 0.6980 chunk 307 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 306 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3725 r_free = 0.3725 target = 0.108091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090461 restraints weight = 70753.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093623 restraints weight = 41582.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.093949 restraints weight = 28238.819| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23902 Z= 0.119 Angle : 0.649 12.798 32662 Z= 0.327 Chirality : 0.046 0.583 3862 Planarity : 0.004 0.057 4134 Dihedral : 6.783 56.417 3574 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 3.70 % Allowed : 21.19 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 3076 helix: 1.01 (0.15), residues: 1206 sheet: -1.67 (0.31), residues: 258 loop : -2.84 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 336 HIS 0.002 0.001 HIS B 359 PHE 0.012 0.001 PHE C 42 TYR 0.012 0.001 TYR A 282 ARG 0.002 0.000 ARG B 337 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 10) link_NAG-ASN : angle 3.76496 ( 30) link_BETA1-4 : bond 0.00706 ( 2) link_BETA1-4 : angle 2.90872 ( 6) hydrogen bonds : bond 0.03917 ( 914) hydrogen bonds : angle 4.74761 ( 2667) SS BOND : bond 0.00313 ( 18) SS BOND : angle 1.19692 ( 36) covalent geometry : bond 0.00264 (23872) covalent geometry : angle 0.63749 (32590) *********************** 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 362 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 275 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8540 (ttm) cc_final: 0.8335 (ttt) REVERT: A 347 MET cc_start: 0.8401 (ppp) cc_final: 0.6978 (mmt) REVERT: A 375 MET cc_start: 0.7046 (tpp) cc_final: 0.6596 (tpp) REVERT: A 385 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7877 (t) REVERT: A 579 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: A 597 MET cc_start: 0.8244 (mmm) cc_final: 0.8040 (ttt) REVERT: A 806 MET cc_start: 0.9070 (tpp) cc_final: 0.8646 (mpp) REVERT: B 105 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: B 308 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.5967 (pp) REVERT: B 337 ARG cc_start: 0.8636 (tpt90) cc_final: 0.8237 (tpt90) REVERT: B 551 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8796 (tt) REVERT: B 656 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7939 (mm-40) REVERT: B 800 ILE cc_start: 0.8417 (pt) cc_final: 0.8179 (tp) REVERT: B 818 MET cc_start: 0.8455 (mpp) cc_final: 0.8174 (mpp) REVERT: C 248 ASP cc_start: 0.7702 (m-30) cc_final: 0.7409 (m-30) REVERT: C 579 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: C 655 MET cc_start: 0.7653 (tmm) cc_final: 0.7210 (tmm) REVERT: C 733 GLU cc_start: 0.8086 (mp0) cc_final: 0.7641 (tp30) REVERT: C 783 MET cc_start: 0.7149 (mtm) cc_final: 0.6796 (mtm) REVERT: D 105 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: D 142 MET cc_start: 0.7506 (tpp) cc_final: 0.7290 (mmt) REVERT: D 308 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6024 (pp) REVERT: D 337 ARG cc_start: 0.8764 (tpt90) cc_final: 0.8432 (tpt90) REVERT: D 656 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8047 (mm-40) REVERT: D 793 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8243 (mt-10) outliers start: 87 outliers final: 62 residues processed: 338 average time/residue: 0.2660 time to fit residues: 153.0173 Evaluate side-chains 333 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 261 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 385 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 518 GLU 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 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 35 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 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 551 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 837 ILE 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 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 798 LEU Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 841 VAL Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain D residue 35 ILE 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 160 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 308 LEU 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 558 VAL Chi-restraints excluded: chain D residue 563 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.9575 > 50: distance: 36 - 53: 32.154 distance: 40 - 58: 25.499 distance: 44 - 63: 31.063 distance: 48 - 53: 31.633 distance: 49 - 74: 31.167 distance: 53 - 54: 15.821 distance: 54 - 55: 24.862 distance: 54 - 57: 59.457 distance: 55 - 56: 35.816 distance: 55 - 58: 17.356 distance: 56 - 82: 30.542 distance: 58 - 59: 7.036 distance: 59 - 60: 15.142 distance: 59 - 62: 9.788 distance: 60 - 61: 16.388 distance: 60 - 63: 7.530 distance: 63 - 64: 5.287 distance: 64 - 65: 23.116 distance: 64 - 67: 46.300 distance: 65 - 66: 26.696 distance: 65 - 74: 10.968 distance: 68 - 70: 39.168 distance: 69 - 71: 39.354 distance: 70 - 72: 23.485 distance: 71 - 73: 39.211 distance: 72 - 73: 45.698 distance: 74 - 75: 40.858 distance: 75 - 76: 9.188 distance: 76 - 77: 12.880 distance: 76 - 82: 7.825 distance: 78 - 79: 41.755 distance: 79 - 80: 10.745 distance: 79 - 81: 12.066 distance: 83 - 84: 44.121 distance: 84 - 85: 32.028 distance: 84 - 89: 20.233 distance: 86 - 88: 51.828 distance: 89 - 90: 27.066 distance: 90 - 91: 20.650 distance: 90 - 93: 26.754 distance: 91 - 92: 45.286 distance: 94 - 96: 28.430 distance: 97 - 98: 25.199 distance: 98 - 99: 40.924 distance: 98 - 101: 35.541 distance: 99 - 100: 40.829 distance: 99 - 105: 33.556 distance: 101 - 102: 39.703 distance: 102 - 104: 40.341 distance: 105 - 106: 49.917 distance: 106 - 107: 48.141 distance: 106 - 109: 41.762 distance: 107 - 108: 18.785 distance: 107 - 110: 26.511 distance: 110 - 111: 5.692 distance: 110 - 116: 46.344 distance: 111 - 112: 8.976 distance: 111 - 114: 27.343 distance: 112 - 113: 31.001 distance: 112 - 117: 26.004 distance: 114 - 115: 41.843 distance: 117 - 118: 24.865 distance: 118 - 119: 45.985 distance: 118 - 121: 59.766 distance: 119 - 120: 39.337 distance: 119 - 122: 32.304