Starting phenix.real_space_refine on Mon May 26 15:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d04_7784/05_2025/6d04_7784.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d04_7784/05_2025/6d04_7784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d04_7784/05_2025/6d04_7784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d04_7784/05_2025/6d04_7784.map" model { file = "/net/cci-nas-00/data/ceres_data/6d04_7784/05_2025/6d04_7784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d04_7784/05_2025/6d04_7784.cif" } resolution = 3.74 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= 0.002 sd= 0.015 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 Ca 2 9.91 5 Fe 4 7.16 5 S 142 5.16 5 C 18252 2.51 5 N 4850 2.21 5 O 5498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 457} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 457} Chain: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.32, per 1000 atoms: 0.53 Number of scatterers: 28748 At special positions: 0 Unit cell: (168.75, 148.5, 166.05, 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) Fe 4 26.01 Ca 2 19.99 S 142 16.00 O 5498 8.00 N 4850 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.02 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.02 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.03 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.02 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.02 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.02 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.03 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.03 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.04 Simple disulfide: pdb=" SG CYS F 240 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG B 802 " - " ASN B 251 " " NAG C 707 " - " ASN C 611 " " NAG D 707 " - " ASN D 611 " " NAG G 1 " - " ASN A 317 " " NAG H 1 " - " ASN A 727 " " NAG I 1 " - " ASN B 317 " " NAG J 1 " - " ASN B 727 " " NAG K 1 " - " ASN C 413 " " NAG L 1 " - " ASN D 413 " Time building additional restraints: 7.17 Conformation dependent library (CDL) restraints added in 3.6 seconds 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6740 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 28 sheets defined 50.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 123 through 136 removed outlier: 4.034A pdb=" N ARG A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 removed outlier: 4.322A pdb=" N THR A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.655A pdb=" N LYS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.573A pdb=" N THR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.628A pdb=" N THR A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.620A pdb=" N SER A 530 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 583 through 603 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 627 removed outlier: 3.679A pdb=" N GLN A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.595A pdb=" N TYR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 681 removed outlier: 3.537A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 708 through 721 removed outlier: 4.125A pdb=" N LEU A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 750 removed outlier: 3.665A pdb=" N PHE A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 136 removed outlier: 4.034A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 removed outlier: 4.322A pdb=" N THR B 143 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 176 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.654A pdb=" N LYS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 439 removed outlier: 3.572A pdb=" N THR B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.629A pdb=" N THR B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.620A pdb=" N SER B 530 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 573 through 580 Processing helix chain 'B' and resid 583 through 603 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 627 removed outlier: 3.678A pdb=" N GLN B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 662 removed outlier: 3.595A pdb=" N TYR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 681 removed outlier: 3.538A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 708 through 721 removed outlier: 4.125A pdb=" N LEU B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN B 721 " --> pdb=" O LYS B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 750 removed outlier: 3.664A pdb=" N PHE B 731 " --> pdb=" O ASN B 727 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 29 removed outlier: 3.959A pdb=" N SER C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL C 29 " --> pdb=" O HIS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 removed outlier: 3.570A pdb=" N CYS C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 128 through 136 removed outlier: 3.569A pdb=" N LEU C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.582A pdb=" N ALA C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 216 through 223 removed outlier: 3.884A pdb=" N TYR C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 275 removed outlier: 3.615A pdb=" N ILE C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 316 through 329 removed outlier: 3.574A pdb=" N VAL C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.519A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.808A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 472 removed outlier: 3.711A pdb=" N LEU C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 removed outlier: 3.552A pdb=" N CYS C 495 " --> pdb=" O SER C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.513A pdb=" N GLY C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.631A pdb=" N LYS C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN C 553 " --> pdb=" O PRO C 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 548 through 553' Processing helix chain 'C' and resid 593 through 609 removed outlier: 4.026A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 652 removed outlier: 3.658A pdb=" N GLY C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'C' and resid 668 through 676 removed outlier: 3.626A pdb=" N GLU C 672 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 29 removed outlier: 3.959A pdb=" N SER D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL D 29 " --> pdb=" O HIS D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 54 removed outlier: 3.570A pdb=" N CYS D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 128 through 136 removed outlier: 3.569A pdb=" N LEU D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.582A pdb=" N ALA D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 216 through 223 removed outlier: 3.884A pdb=" N TYR D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 275 removed outlier: 3.616A pdb=" N ILE D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS D 273 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.575A pdb=" N VAL D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 373 through 384 removed outlier: 3.519A pdb=" N ALA D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 removed outlier: 3.807A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.711A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.552A pdb=" N CYS D 495 " --> pdb=" O SER D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.513A pdb=" N GLY D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 548 through 553 removed outlier: 3.630A pdb=" N LYS D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN D 553 " --> pdb=" O PRO D 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 548 through 553' Processing helix chain 'D' and resid 593 through 609 removed outlier: 4.025A pdb=" N LEU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.657A pdb=" N GLY D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 661 Processing helix chain 'D' and resid 668 through 676 removed outlier: 3.625A pdb=" N GLU D 672 " --> pdb=" O SER D 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 4.349A pdb=" N TYR E 200 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 240 Processing helix chain 'E' and resid 240 through 255 Processing helix chain 'E' and resid 266 through 308 removed outlier: 3.816A pdb=" N LYS E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 335 removed outlier: 4.569A pdb=" N LYS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET E 335 " --> pdb=" O ASP E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 362 removed outlier: 3.594A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 406 Processing helix chain 'E' and resid 415 through 477 removed outlier: 3.620A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY E 463 " --> pdb=" O GLY E 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG E 468 " --> pdb=" O HIS E 464 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR E 477 " --> pdb=" O ILE E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 510 removed outlier: 5.466A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 512 No H-bonds generated for 'chain 'E' and resid 511 through 512' Processing helix chain 'E' and resid 513 through 517 removed outlier: 3.967A pdb=" N LEU E 516 " --> pdb=" O TYR E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 566 removed outlier: 4.035A pdb=" N ASP E 524 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 590 removed outlier: 3.792A pdb=" N ASP E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 633 removed outlier: 3.716A pdb=" N ILE E 633 " --> pdb=" O VAL E 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 212 removed outlier: 4.348A pdb=" N TYR F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 240 Processing helix chain 'F' and resid 240 through 255 Processing helix chain 'F' and resid 266 through 308 removed outlier: 3.816A pdb=" N LYS F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS F 288 " --> pdb=" O CYS F 284 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS F 291 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 335 removed outlier: 4.569A pdb=" N LYS F 326 " --> pdb=" O PHE F 322 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F 335 " --> pdb=" O ASP F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 362 removed outlier: 3.594A pdb=" N LYS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 406 Processing helix chain 'F' and resid 415 through 477 removed outlier: 3.620A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY F 463 " --> pdb=" O GLY F 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG F 468 " --> pdb=" O HIS F 464 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP F 474 " --> pdb=" O SER F 470 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR F 477 " --> pdb=" O ILE F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 510 removed outlier: 5.466A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 512 No H-bonds generated for 'chain 'F' and resid 511 through 512' Processing helix chain 'F' and resid 513 through 517 removed outlier: 3.967A pdb=" N LEU F 516 " --> pdb=" O TYR F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 566 removed outlier: 4.034A pdb=" N ASP F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 590 removed outlier: 3.791A pdb=" N ASP F 578 " --> pdb=" O GLN F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 633 removed outlier: 3.715A pdb=" N ILE F 633 " --> pdb=" O VAL F 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 193 removed outlier: 4.118A pdb=" N SER A 447 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS A 401 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 449 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL A 403 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA A 451 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 405 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TRP A 453 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA A 407 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA A 478 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR A 402 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 480 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 406 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 214 removed outlier: 7.389A pdb=" N VAL A 200 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.778A pdb=" N ASP A 352 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG A 364 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 193 removed outlier: 4.119A pdb=" N SER B 447 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS B 401 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 449 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 403 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA B 451 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 405 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TRP B 453 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA B 407 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA B 478 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B 402 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR B 480 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 406 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 210 through 214 removed outlier: 7.390A pdb=" N VAL B 200 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.778A pdb=" N ASP B 352 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B 364 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 10 Processing sheet with id=AB3, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.932A pdb=" N VAL C 60 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 251 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.818A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA C 99 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 226 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.818A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 347 removed outlier: 6.060A pdb=" N VAL C 342 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 369 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP C 344 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA C 371 " --> pdb=" O TRP C 344 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 346 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 388 through 391 removed outlier: 6.429A pdb=" N VAL C 587 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 483 through 484 removed outlier: 7.210A pdb=" N SER C 449 " --> pdb=" O CYS C 484 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS C 450 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS C 534 " --> pdb=" O CYS C 450 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA C 430 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 562 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 569 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 483 through 484 removed outlier: 7.210A pdb=" N SER C 449 " --> pdb=" O CYS C 484 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS C 450 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS C 534 " --> pdb=" O CYS C 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 5 through 10 Processing sheet with id=AC2, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.933A pdb=" N VAL D 60 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 251 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.818A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA D 99 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 226 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.818A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 342 through 347 removed outlier: 6.059A pdb=" N VAL D 342 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL D 369 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP D 344 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA D 371 " --> pdb=" O TRP D 344 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA D 346 " --> pdb=" O ALA D 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 388 through 391 removed outlier: 6.428A pdb=" N VAL D 587 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 483 through 484 removed outlier: 7.209A pdb=" N SER D 449 " --> pdb=" O CYS D 484 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS D 450 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYS D 534 " --> pdb=" O CYS D 450 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA D 430 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 562 " --> pdb=" O ALA D 430 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS D 569 " --> pdb=" O LEU D 561 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 483 through 484 removed outlier: 7.209A pdb=" N SER D 449 " --> pdb=" O CYS D 484 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS D 450 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYS D 534 " --> pdb=" O CYS D 450 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 180 through 181 removed outlier: 4.082A pdb=" N ILE E 180 " --> pdb=" O ILE E 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 180 through 181 removed outlier: 4.082A pdb=" N ILE F 180 " --> pdb=" O ILE F 189 " (cutoff:3.500A) 1434 hydrogen bonds defined for protein. 4194 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: 10.29 Time building geometry restraints manager: 8.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8531 1.34 - 1.46: 6384 1.46 - 1.58: 14253 1.58 - 1.70: 0 1.70 - 1.83: 192 Bond restraints: 29360 Sorted by residual: bond pdb=" CA ARG B 155 " pdb=" CB ARG B 155 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.46e-02 4.69e+03 7.32e+00 bond pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 1.524 1.563 -0.039 1.46e-02 4.69e+03 7.13e+00 bond pdb=" C1 NAG C 707 " pdb=" O5 NAG C 707 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" N ASN B 236 " pdb=" CA ASN B 236 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.79e+00 bond pdb=" N ASN A 236 " pdb=" CA ASN A 236 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.71e+00 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 38540 2.78 - 5.56: 1000 5.56 - 8.34: 92 8.34 - 11.12: 24 11.12 - 13.89: 8 Bond angle restraints: 39664 Sorted by residual: angle pdb=" CA TYR E 422 " pdb=" CB TYR E 422 " pdb=" CG TYR E 422 " ideal model delta sigma weight residual 113.90 127.79 -13.89 1.80e+00 3.09e-01 5.96e+01 angle pdb=" CA TYR F 422 " pdb=" CB TYR F 422 " pdb=" CG TYR F 422 " ideal model delta sigma weight residual 113.90 127.76 -13.86 1.80e+00 3.09e-01 5.93e+01 angle pdb=" C GLY C 502 " pdb=" N LEU C 503 " pdb=" CA LEU C 503 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY D 502 " pdb=" N LEU D 503 " pdb=" CA LEU D 503 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C ASN C 461 " pdb=" N ILE C 462 " pdb=" CA ILE C 462 " ideal model delta sigma weight residual 120.24 123.28 -3.04 6.30e-01 2.52e+00 2.32e+01 ... (remaining 39659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 17249 21.89 - 43.78: 632 43.78 - 65.67: 109 65.67 - 87.56: 32 87.56 - 109.46: 20 Dihedral angle restraints: 18042 sinusoidal: 7570 harmonic: 10472 Sorted by residual: dihedral pdb=" CA GLN F 317 " pdb=" C GLN F 317 " pdb=" N THR F 318 " pdb=" CA THR F 318 " ideal model delta harmonic sigma weight residual 180.00 92.36 87.64 0 5.00e+00 4.00e-02 3.07e+02 dihedral pdb=" CA GLN E 317 " pdb=" C GLN E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta harmonic sigma weight residual 180.00 92.41 87.59 0 5.00e+00 4.00e-02 3.07e+02 dihedral pdb=" CA ASP F 407 " pdb=" C ASP F 407 " pdb=" N GLY F 408 " pdb=" CA GLY F 408 " ideal model delta harmonic sigma weight residual -180.00 -93.39 -86.61 0 5.00e+00 4.00e-02 3.00e+02 ... (remaining 18039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 4324 0.187 - 0.374: 22 0.374 - 0.561: 4 0.561 - 0.748: 2 0.748 - 0.934: 2 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 727 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 727 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 251 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 4351 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 422 " 0.049 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR F 422 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR F 422 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 422 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 422 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 422 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 422 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 422 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 422 " -0.049 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR E 422 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR E 422 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 422 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 422 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 422 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 422 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 422 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 251 " -0.035 2.00e-02 2.50e+03 3.27e-02 1.34e+01 pdb=" CG ASN B 251 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 251 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 251 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG B 802 " -0.035 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 199 2.58 - 3.16: 22835 3.16 - 3.74: 43443 3.74 - 4.32: 59605 4.32 - 4.90: 97765 Nonbonded interactions: 223847 Sorted by model distance: nonbonded pdb="FE FE D 703 " pdb=" O3 CO3 D 704 " model vdw 2.001 2.260 nonbonded pdb="FE FE C 703 " pdb=" O3 CO3 C 704 " model vdw 2.012 2.260 nonbonded pdb=" OD1 ASP D 63 " pdb="FE FE D 703 " model vdw 2.035 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.039 2.260 nonbonded pdb=" OD1 ASP C 63 " pdb="FE FE C 703 " model vdw 2.043 2.260 ... (remaining 223842 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.300 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: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 59.660 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.008 0.074 29422 Z= 0.356 Angle : 1.110 21.991 39804 Z= 0.613 Chirality : 0.062 0.934 4354 Planarity : 0.007 0.071 5106 Dihedral : 12.378 109.455 11164 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.21 % Allowed : 6.30 % Favored : 92.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % 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: -3.02 (0.11), residues: 3560 helix: -2.00 (0.10), residues: 1672 sheet: -1.14 (0.26), residues: 336 loop : -2.07 (0.13), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP D 358 HIS 0.011 0.002 HIS D 585 PHE 0.037 0.003 PHE A 176 TYR 0.069 0.003 TYR E 422 ARG 0.023 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.01844 ( 10) link_NAG-ASN : angle 8.11245 ( 30) link_BETA1-4 : bond 0.01240 ( 6) link_BETA1-4 : angle 7.76895 ( 18) hydrogen bonds : bond 0.14266 ( 1414) hydrogen bonds : angle 7.95272 ( 4194) SS BOND : bond 0.00545 ( 46) SS BOND : angle 1.86529 ( 92) covalent geometry : bond 0.00813 (29360) covalent geometry : angle 1.07309 (39664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 394 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9117 (pp) cc_final: 0.8822 (pp) REVERT: A 510 MET cc_start: 0.8501 (mtp) cc_final: 0.8251 (mtm) REVERT: A 570 MET cc_start: 0.8531 (ttm) cc_final: 0.8230 (ttm) REVERT: A 574 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (pttm) REVERT: A 671 MET cc_start: 0.8622 (mmm) cc_final: 0.8290 (mmt) REVERT: B 126 ASP cc_start: 0.8253 (t70) cc_final: 0.7698 (t0) REVERT: C 309 MET cc_start: 0.8719 (ttm) cc_final: 0.8412 (mtp) REVERT: C 367 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7833 (mt-10) REVERT: C 477 ASP cc_start: 0.7388 (p0) cc_final: 0.6827 (t0) REVERT: C 514 TYR cc_start: 0.7794 (m-10) cc_final: 0.7373 (m-80) REVERT: D 309 MET cc_start: 0.8835 (ttm) cc_final: 0.8457 (mtp) REVERT: D 514 TYR cc_start: 0.7757 (m-10) cc_final: 0.7307 (m-80) REVERT: E 324 MET cc_start: 0.7810 (mmm) cc_final: 0.6493 (tpp) REVERT: E 596 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6688 (tm-30) REVERT: E 608 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8599 (mm) REVERT: F 205 PHE cc_start: 0.8483 (t80) cc_final: 0.8196 (t80) REVERT: F 414 VAL cc_start: 0.6230 (m) cc_final: 0.5935 (m) REVERT: F 508 GLU cc_start: 0.7659 (tt0) cc_final: 0.7434 (tp30) REVERT: F 631 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6670 (tp30) outliers start: 38 outliers final: 4 residues processed: 428 average time/residue: 0.4418 time to fit residues: 287.6055 Evaluate side-chains 145 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain E residue 608 ILE Chi-restraints excluded: chain F residue 600 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 236 ASN A 275 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 640 GLN A 715 ASN B 148 ASN B 197 GLN B 236 ASN B 275 ASN B 401 HIS B 483 ASN B 608 ASN B 626 ASN B 640 GLN B 715 ASN B 721 GLN C 25 HIS C 55 ASN C 300 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN C 604 GLN C 618 ASN D 55 ASN D 300 HIS ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 604 GLN D 618 ASN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 ASN E 346 GLN E 364 GLN E 397 HIS E 444 ASN E 456 ASN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN F 397 HIS F 444 ASN F 456 ASN F 527 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087551 restraints weight = 55332.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.086541 restraints weight = 67409.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.087519 restraints weight = 71230.231| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 29422 Z= 0.254 Angle : 0.763 17.324 39804 Z= 0.398 Chirality : 0.049 0.666 4354 Planarity : 0.005 0.056 5106 Dihedral : 8.554 82.606 4221 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 2.65 % Allowed : 9.59 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % 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: -1.18 (0.13), residues: 3560 helix: 0.06 (0.12), residues: 1702 sheet: -0.95 (0.27), residues: 332 loop : -1.67 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 740 HIS 0.008 0.002 HIS E 222 PHE 0.038 0.002 PHE E 521 TYR 0.054 0.002 TYR F 422 ARG 0.008 0.001 ARG E 217 Details of bonding type rmsd link_NAG-ASN : bond 0.01252 ( 10) link_NAG-ASN : angle 5.75267 ( 30) link_BETA1-4 : bond 0.00766 ( 6) link_BETA1-4 : angle 4.20646 ( 18) hydrogen bonds : bond 0.07082 ( 1414) hydrogen bonds : angle 5.34174 ( 4194) SS BOND : bond 0.00716 ( 46) SS BOND : angle 1.36421 ( 92) covalent geometry : bond 0.00584 (29360) covalent geometry : angle 0.73947 (39664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 149 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8163 (mtp) cc_final: 0.7153 (ttm) REVERT: A 574 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8413 (pttm) REVERT: A 671 MET cc_start: 0.8821 (mmm) cc_final: 0.8399 (mmt) REVERT: B 126 ASP cc_start: 0.7774 (t70) cc_final: 0.7465 (t0) REVERT: B 232 LEU cc_start: 0.8524 (tp) cc_final: 0.8309 (tp) REVERT: C 62 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8447 (pp) REVERT: C 235 VAL cc_start: 0.9021 (m) cc_final: 0.8807 (p) REVERT: C 309 MET cc_start: 0.8765 (ttm) cc_final: 0.8517 (mtp) REVERT: C 477 ASP cc_start: 0.7405 (p0) cc_final: 0.6861 (t0) REVERT: C 499 MET cc_start: 0.8406 (ptm) cc_final: 0.8062 (ptm) REVERT: C 514 TYR cc_start: 0.7800 (m-10) cc_final: 0.7279 (m-80) REVERT: D 62 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8504 (pp) REVERT: D 309 MET cc_start: 0.8790 (ttm) cc_final: 0.8448 (mtp) REVERT: D 477 ASP cc_start: 0.7378 (p0) cc_final: 0.6919 (t0) REVERT: D 499 MET cc_start: 0.8400 (ptm) cc_final: 0.7930 (ptm) REVERT: D 514 TYR cc_start: 0.7788 (m-10) cc_final: 0.7358 (m-80) REVERT: E 279 GLU cc_start: 0.7551 (mp0) cc_final: 0.7027 (mp0) REVERT: E 324 MET cc_start: 0.6927 (mmm) cc_final: 0.6701 (mmp) REVERT: E 346 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8368 (pp30) REVERT: E 357 MET cc_start: 0.7454 (mmm) cc_final: 0.7092 (mmm) REVERT: F 205 PHE cc_start: 0.8022 (t80) cc_final: 0.7751 (t80) outliers start: 83 outliers final: 39 residues processed: 222 average time/residue: 0.3806 time to fit residues: 137.6767 Evaluate side-chains 148 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 626 GLN Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 251 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 411 ASN D 411 ASN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089832 restraints weight = 54472.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.088562 restraints weight = 61935.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.089593 restraints weight = 70563.769| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29422 Z= 0.134 Angle : 0.621 15.526 39804 Z= 0.316 Chirality : 0.044 0.596 4354 Planarity : 0.004 0.044 5106 Dihedral : 7.329 71.411 4215 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.01 % Allowed : 11.13 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % 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: -0.29 (0.13), residues: 3560 helix: 0.95 (0.12), residues: 1682 sheet: -0.71 (0.29), residues: 320 loop : -1.35 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 740 HIS 0.005 0.001 HIS F 628 PHE 0.016 0.001 PHE D 84 TYR 0.044 0.001 TYR F 422 ARG 0.004 0.000 ARG D 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00843 ( 10) link_NAG-ASN : angle 5.38621 ( 30) link_BETA1-4 : bond 0.00829 ( 6) link_BETA1-4 : angle 4.41239 ( 18) hydrogen bonds : bond 0.06071 ( 1414) hydrogen bonds : angle 4.86013 ( 4194) SS BOND : bond 0.00257 ( 46) SS BOND : angle 1.02942 ( 92) covalent geometry : bond 0.00272 (29360) covalent geometry : angle 0.59462 (39664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 133 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8039 (mtp) cc_final: 0.7173 (ttm) REVERT: A 671 MET cc_start: 0.8738 (mmm) cc_final: 0.8342 (mmt) REVERT: B 126 ASP cc_start: 0.7580 (t70) cc_final: 0.7204 (t0) REVERT: B 624 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7795 (m-30) REVERT: C 62 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8295 (pp) REVERT: C 235 VAL cc_start: 0.9028 (m) cc_final: 0.8814 (p) REVERT: C 309 MET cc_start: 0.8702 (ttm) cc_final: 0.8414 (mtp) REVERT: C 477 ASP cc_start: 0.7271 (p0) cc_final: 0.6850 (t0) REVERT: C 499 MET cc_start: 0.8463 (ptm) cc_final: 0.7970 (ptm) REVERT: C 514 TYR cc_start: 0.7976 (m-10) cc_final: 0.7373 (m-80) REVERT: D 309 MET cc_start: 0.8747 (ttm) cc_final: 0.8400 (mtp) REVERT: D 477 ASP cc_start: 0.7223 (p0) cc_final: 0.6892 (t0) REVERT: D 499 MET cc_start: 0.8499 (ptm) cc_final: 0.8144 (ptm) REVERT: D 514 TYR cc_start: 0.7884 (m-10) cc_final: 0.7315 (m-80) REVERT: E 205 PHE cc_start: 0.8258 (t80) cc_final: 0.7807 (t80) REVERT: E 279 GLU cc_start: 0.7814 (mp0) cc_final: 0.6957 (mp0) REVERT: E 324 MET cc_start: 0.6605 (mmm) cc_final: 0.6227 (mmp) REVERT: F 205 PHE cc_start: 0.8072 (t80) cc_final: 0.7593 (t80) REVERT: F 422 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7507 (m-80) outliers start: 63 outliers final: 31 residues processed: 187 average time/residue: 0.3848 time to fit residues: 121.2844 Evaluate side-chains 141 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 65 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 260 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 0.0870 chunk 328 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 383 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 ASN E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088608 restraints weight = 55098.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.087478 restraints weight = 64286.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088290 restraints weight = 73519.089| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29422 Z= 0.164 Angle : 0.628 14.943 39804 Z= 0.320 Chirality : 0.045 0.606 4354 Planarity : 0.003 0.042 5106 Dihedral : 6.828 69.783 4211 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.59 % Allowed : 11.13 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % 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: 0.12 (0.14), residues: 3560 helix: 1.36 (0.12), residues: 1694 sheet: -0.64 (0.29), residues: 320 loop : -1.21 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 740 HIS 0.005 0.001 HIS B 475 PHE 0.016 0.001 PHE C 22 TYR 0.042 0.001 TYR E 218 ARG 0.005 0.000 ARG D 7 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 10) link_NAG-ASN : angle 5.18338 ( 30) link_BETA1-4 : bond 0.00815 ( 6) link_BETA1-4 : angle 4.39384 ( 18) hydrogen bonds : bond 0.05938 ( 1414) hydrogen bonds : angle 4.71383 ( 4194) SS BOND : bond 0.00617 ( 46) SS BOND : angle 1.72452 ( 92) covalent geometry : bond 0.00368 (29360) covalent geometry : angle 0.59934 (39664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 118 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8139 (mtm) cc_final: 0.7229 (ttm) REVERT: A 671 MET cc_start: 0.8858 (mmm) cc_final: 0.8539 (mmt) REVERT: B 126 ASP cc_start: 0.7611 (t70) cc_final: 0.7289 (t0) REVERT: B 364 ARG cc_start: 0.8588 (mmt180) cc_final: 0.8357 (mmt-90) REVERT: B 624 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: C 62 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8248 (pp) REVERT: C 112 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8752 (tm) REVERT: C 235 VAL cc_start: 0.9070 (m) cc_final: 0.8850 (p) REVERT: C 309 MET cc_start: 0.8705 (ttm) cc_final: 0.8421 (mtp) REVERT: C 477 ASP cc_start: 0.7372 (p0) cc_final: 0.6855 (t0) REVERT: C 499 MET cc_start: 0.8448 (ptm) cc_final: 0.8000 (ptm) REVERT: C 514 TYR cc_start: 0.8010 (m-10) cc_final: 0.7360 (m-80) REVERT: D 62 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8372 (pp) REVERT: D 112 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8969 (tm) REVERT: D 309 MET cc_start: 0.8683 (ttm) cc_final: 0.8281 (mtp) REVERT: D 338 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: D 477 ASP cc_start: 0.7360 (p0) cc_final: 0.6816 (t0) REVERT: D 499 MET cc_start: 0.8462 (ptm) cc_final: 0.8166 (ptm) REVERT: D 514 TYR cc_start: 0.7957 (m-10) cc_final: 0.7368 (m-80) REVERT: E 205 PHE cc_start: 0.7941 (t80) cc_final: 0.7543 (t80) REVERT: E 263 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: E 324 MET cc_start: 0.6864 (mmm) cc_final: 0.6649 (mmp) REVERT: E 346 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8228 (pp30) REVERT: E 352 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8866 (mt) REVERT: F 205 PHE cc_start: 0.8096 (t80) cc_final: 0.7557 (t80) REVERT: F 422 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: F 506 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7168 (tp) outliers start: 81 outliers final: 40 residues processed: 192 average time/residue: 0.3731 time to fit residues: 120.4057 Evaluate side-chains 157 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 338 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 316 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 383 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.089955 restraints weight = 54550.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.088872 restraints weight = 64457.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.089976 restraints weight = 69415.926| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29422 Z= 0.129 Angle : 0.593 15.163 39804 Z= 0.301 Chirality : 0.044 0.704 4354 Planarity : 0.003 0.040 5106 Dihedral : 6.574 68.243 4210 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.65 % Allowed : 11.51 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % 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: 0.47 (0.14), residues: 3560 helix: 1.71 (0.12), residues: 1696 sheet: -0.62 (0.29), residues: 320 loop : -1.10 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 PHE 0.015 0.001 PHE D 84 TYR 0.036 0.001 TYR F 218 ARG 0.008 0.000 ARG E 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 10) link_NAG-ASN : angle 4.96853 ( 30) link_BETA1-4 : bond 0.00663 ( 6) link_BETA1-4 : angle 4.31636 ( 18) hydrogen bonds : bond 0.05539 ( 1414) hydrogen bonds : angle 4.51982 ( 4194) SS BOND : bond 0.00243 ( 46) SS BOND : angle 1.49886 ( 92) covalent geometry : bond 0.00272 (29360) covalent geometry : angle 0.56658 (39664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 122 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8491 (m-40) REVERT: A 432 MET cc_start: 0.8119 (mtm) cc_final: 0.7325 (ttm) REVERT: A 671 MET cc_start: 0.8836 (mmm) cc_final: 0.8576 (mmt) REVERT: B 126 ASP cc_start: 0.7507 (t70) cc_final: 0.7182 (t0) REVERT: B 624 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: C 62 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8170 (pp) REVERT: C 112 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8734 (tm) REVERT: C 235 VAL cc_start: 0.9098 (m) cc_final: 0.8890 (p) REVERT: C 309 MET cc_start: 0.8694 (ttm) cc_final: 0.8377 (mtp) REVERT: C 477 ASP cc_start: 0.7582 (p0) cc_final: 0.7084 (t0) REVERT: C 499 MET cc_start: 0.8427 (ptm) cc_final: 0.8025 (ptm) REVERT: C 514 TYR cc_start: 0.8026 (m-10) cc_final: 0.7375 (m-80) REVERT: D 62 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8293 (pp) REVERT: D 112 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8938 (tm) REVERT: D 309 MET cc_start: 0.8557 (ttm) cc_final: 0.8265 (mtp) REVERT: D 338 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7068 (mt-10) REVERT: D 477 ASP cc_start: 0.7641 (p0) cc_final: 0.7177 (t0) REVERT: D 499 MET cc_start: 0.8254 (ptm) cc_final: 0.7870 (ptm) REVERT: D 514 TYR cc_start: 0.8020 (m-10) cc_final: 0.7429 (m-80) REVERT: E 205 PHE cc_start: 0.7903 (t80) cc_final: 0.7571 (t80) REVERT: E 263 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: E 352 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8851 (mt) REVERT: F 205 PHE cc_start: 0.7879 (t80) cc_final: 0.7225 (t80) REVERT: F 263 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: F 422 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: F 506 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7160 (tp) outliers start: 83 outliers final: 45 residues processed: 198 average time/residue: 0.3853 time to fit residues: 129.1301 Evaluate side-chains 163 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 572 ASN Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 32 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 chunk 260 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 721 GLN B 723 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.088665 restraints weight = 54780.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087811 restraints weight = 65739.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088561 restraints weight = 72729.018| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29422 Z= 0.150 Angle : 0.601 13.473 39804 Z= 0.304 Chirality : 0.044 0.598 4354 Planarity : 0.003 0.039 5106 Dihedral : 6.398 67.072 4210 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.69 % Allowed : 12.40 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3560 helix: 1.86 (0.12), residues: 1690 sheet: -0.60 (0.29), residues: 320 loop : -1.05 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 PHE 0.016 0.001 PHE C 22 TYR 0.037 0.001 TYR E 218 ARG 0.004 0.000 ARG A 623 Details of bonding type rmsd link_NAG-ASN : bond 0.01072 ( 10) link_NAG-ASN : angle 4.73870 ( 30) link_BETA1-4 : bond 0.00912 ( 6) link_BETA1-4 : angle 4.43221 ( 18) hydrogen bonds : bond 0.05528 ( 1414) hydrogen bonds : angle 4.45956 ( 4194) SS BOND : bond 0.00608 ( 46) SS BOND : angle 1.44363 ( 92) covalent geometry : bond 0.00332 (29360) covalent geometry : angle 0.57645 (39664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 111 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 MET cc_start: 0.8901 (mmm) cc_final: 0.8660 (mmt) REVERT: B 126 ASP cc_start: 0.7527 (t70) cc_final: 0.7241 (t0) REVERT: B 364 ARG cc_start: 0.8709 (mpt180) cc_final: 0.8269 (mpt180) REVERT: B 624 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: C 62 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8214 (pp) REVERT: C 112 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8747 (tm) REVERT: C 235 VAL cc_start: 0.9117 (m) cc_final: 0.8906 (p) REVERT: C 309 MET cc_start: 0.8708 (ttm) cc_final: 0.8376 (mtp) REVERT: C 477 ASP cc_start: 0.7570 (p0) cc_final: 0.7057 (t0) REVERT: C 499 MET cc_start: 0.8281 (ptm) cc_final: 0.7925 (ptm) REVERT: C 514 TYR cc_start: 0.8060 (m-10) cc_final: 0.7393 (m-80) REVERT: C 643 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7557 (p0) REVERT: D 62 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8312 (pp) REVERT: D 112 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8936 (tm) REVERT: D 235 VAL cc_start: 0.9060 (m) cc_final: 0.8859 (p) REVERT: D 309 MET cc_start: 0.8555 (ttm) cc_final: 0.8203 (mtp) REVERT: D 499 MET cc_start: 0.8317 (ptm) cc_final: 0.7936 (ptm) REVERT: D 514 TYR cc_start: 0.8031 (m-10) cc_final: 0.7438 (m-80) REVERT: E 205 PHE cc_start: 0.7946 (t80) cc_final: 0.7406 (t80) REVERT: E 346 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8259 (pp30) REVERT: E 352 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8869 (mt) REVERT: E 357 MET cc_start: 0.7344 (mmm) cc_final: 0.7056 (mmt) REVERT: F 205 PHE cc_start: 0.7662 (t80) cc_final: 0.7162 (t80) REVERT: F 422 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: F 506 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7175 (tp) outliers start: 84 outliers final: 46 residues processed: 191 average time/residue: 0.3455 time to fit residues: 111.6032 Evaluate side-chains 156 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 308 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 312 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN C 451 HIS D 451 HIS E 252 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084771 restraints weight = 55012.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.083419 restraints weight = 64488.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.084591 restraints weight = 67501.482| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 29422 Z= 0.262 Angle : 0.701 16.367 39804 Z= 0.357 Chirality : 0.048 0.656 4354 Planarity : 0.004 0.041 5106 Dihedral : 6.531 67.788 4210 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.56 % Allowed : 12.98 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % 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: 0.38 (0.14), residues: 3560 helix: 1.67 (0.12), residues: 1708 sheet: -0.88 (0.27), residues: 364 loop : -1.15 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 740 HIS 0.007 0.001 HIS B 401 PHE 0.025 0.002 PHE A 442 TYR 0.031 0.002 TYR F 525 ARG 0.008 0.001 ARG E 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00737 ( 10) link_NAG-ASN : angle 5.10349 ( 30) link_BETA1-4 : bond 0.00621 ( 6) link_BETA1-4 : angle 4.42612 ( 18) hydrogen bonds : bond 0.06161 ( 1414) hydrogen bonds : angle 4.73722 ( 4194) SS BOND : bond 0.00464 ( 46) SS BOND : angle 1.49309 ( 92) covalent geometry : bond 0.00618 (29360) covalent geometry : angle 0.67822 (39664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 108 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8705 (pp) REVERT: B 126 ASP cc_start: 0.7981 (t70) cc_final: 0.7636 (t0) REVERT: B 364 ARG cc_start: 0.8351 (mpt180) cc_final: 0.8060 (mmt180) REVERT: C 62 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8335 (pp) REVERT: C 112 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8825 (tm) REVERT: C 309 MET cc_start: 0.8745 (ttm) cc_final: 0.8414 (mtp) REVERT: C 514 TYR cc_start: 0.8131 (m-10) cc_final: 0.7559 (m-10) REVERT: C 540 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8801 (mp10) REVERT: D 62 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8471 (pp) REVERT: D 112 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8938 (tm) REVERT: D 309 MET cc_start: 0.8743 (ttm) cc_final: 0.8276 (mtp) REVERT: D 313 MET cc_start: 0.9091 (tpp) cc_final: 0.8700 (ttt) REVERT: D 514 TYR cc_start: 0.7994 (m-10) cc_final: 0.7518 (m-80) REVERT: E 205 PHE cc_start: 0.7993 (t80) cc_final: 0.7494 (t80) REVERT: E 263 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: E 352 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8891 (mt) REVERT: F 205 PHE cc_start: 0.7880 (t80) cc_final: 0.7325 (t80) REVERT: F 263 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: F 357 MET cc_start: 0.7303 (mmt) cc_final: 0.7087 (mmt) REVERT: F 422 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7183 (m-80) outliers start: 80 outliers final: 56 residues processed: 182 average time/residue: 0.3599 time to fit residues: 110.7929 Evaluate side-chains 159 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 93 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 344 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 319 optimal weight: 7.9990 chunk 299 optimal weight: 9.9990 chunk 297 optimal weight: 4.9990 chunk 238 optimal weight: 0.0980 chunk 326 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN D 383 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088812 restraints weight = 54777.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.088384 restraints weight = 66516.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089255 restraints weight = 66694.597| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29422 Z= 0.122 Angle : 0.591 13.945 39804 Z= 0.297 Chirality : 0.043 0.575 4354 Planarity : 0.003 0.040 5106 Dihedral : 6.305 65.840 4210 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.17 % Allowed : 13.65 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3560 helix: 1.97 (0.12), residues: 1696 sheet: -0.66 (0.29), residues: 340 loop : -0.96 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 453 HIS 0.003 0.001 HIS C 598 PHE 0.015 0.001 PHE D 84 TYR 0.028 0.001 TYR F 525 ARG 0.006 0.000 ARG E 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 10) link_NAG-ASN : angle 4.57968 ( 30) link_BETA1-4 : bond 0.00741 ( 6) link_BETA1-4 : angle 4.13694 ( 18) hydrogen bonds : bond 0.05326 ( 1414) hydrogen bonds : angle 4.37503 ( 4194) SS BOND : bond 0.00285 ( 46) SS BOND : angle 1.11148 ( 92) covalent geometry : bond 0.00253 (29360) covalent geometry : angle 0.56915 (39664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 108 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8143 (mtm) cc_final: 0.7580 (ttm) REVERT: B 126 ASP cc_start: 0.7705 (t70) cc_final: 0.7456 (t0) REVERT: B 364 ARG cc_start: 0.7866 (mpt180) cc_final: 0.7466 (mmt180) REVERT: C 62 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8189 (pp) REVERT: C 112 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8789 (tm) REVERT: C 309 MET cc_start: 0.8670 (ttm) cc_final: 0.8355 (mtp) REVERT: C 499 MET cc_start: 0.8239 (ptm) cc_final: 0.8012 (ptm) REVERT: C 514 TYR cc_start: 0.7995 (m-10) cc_final: 0.7588 (m-80) REVERT: D 62 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8559 (pp) REVERT: D 112 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8931 (tm) REVERT: D 309 MET cc_start: 0.8672 (ttm) cc_final: 0.8345 (mtp) REVERT: D 514 TYR cc_start: 0.8012 (m-10) cc_final: 0.7571 (m-80) REVERT: E 205 PHE cc_start: 0.7789 (t80) cc_final: 0.7435 (t80) REVERT: E 263 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: E 352 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8856 (mt) REVERT: F 205 PHE cc_start: 0.7511 (t80) cc_final: 0.7034 (t80) REVERT: F 263 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: F 357 MET cc_start: 0.7277 (mmm) cc_final: 0.7040 (mmt) REVERT: F 422 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6996 (m-80) outliers start: 68 outliers final: 52 residues processed: 171 average time/residue: 0.3463 time to fit residues: 102.6742 Evaluate side-chains 154 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 322 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN E 289 ASN E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088572 restraints weight = 54659.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.087417 restraints weight = 63158.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088441 restraints weight = 67314.423| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29422 Z= 0.125 Angle : 0.580 13.141 39804 Z= 0.291 Chirality : 0.043 0.499 4354 Planarity : 0.003 0.040 5106 Dihedral : 6.151 63.771 4210 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.17 % Allowed : 13.84 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % 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: 0.88 (0.14), residues: 3560 helix: 2.09 (0.12), residues: 1698 sheet: -0.60 (0.29), residues: 340 loop : -0.89 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 740 HIS 0.003 0.001 HIS B 475 PHE 0.015 0.001 PHE C 22 TYR 0.025 0.001 TYR F 525 ARG 0.005 0.000 ARG E 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 10) link_NAG-ASN : angle 4.37064 ( 30) link_BETA1-4 : bond 0.00640 ( 6) link_BETA1-4 : angle 4.04685 ( 18) hydrogen bonds : bond 0.05223 ( 1414) hydrogen bonds : angle 4.30400 ( 4194) SS BOND : bond 0.00278 ( 46) SS BOND : angle 1.03541 ( 92) covalent geometry : bond 0.00266 (29360) covalent geometry : angle 0.55934 (39664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 107 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8114 (mtm) cc_final: 0.7572 (ttm) REVERT: B 126 ASP cc_start: 0.7685 (t70) cc_final: 0.7446 (t0) REVERT: B 679 MET cc_start: 0.8790 (mtt) cc_final: 0.8508 (mtm) REVERT: C 62 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8206 (pp) REVERT: C 112 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8806 (tm) REVERT: C 309 MET cc_start: 0.8671 (ttm) cc_final: 0.8342 (mtp) REVERT: C 499 MET cc_start: 0.8255 (ptm) cc_final: 0.8026 (ptm) REVERT: C 514 TYR cc_start: 0.8095 (m-10) cc_final: 0.7628 (m-80) REVERT: D 62 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8553 (pp) REVERT: D 112 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8927 (tm) REVERT: D 309 MET cc_start: 0.8672 (ttm) cc_final: 0.8314 (mtp) REVERT: D 313 MET cc_start: 0.9030 (tpp) cc_final: 0.8607 (ttt) REVERT: D 354 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8431 (tttm) REVERT: D 514 TYR cc_start: 0.8050 (m-10) cc_final: 0.7626 (m-80) REVERT: E 205 PHE cc_start: 0.7916 (t80) cc_final: 0.7532 (t80) REVERT: E 263 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: E 346 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8090 (pp30) REVERT: E 352 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8850 (mt) REVERT: F 205 PHE cc_start: 0.7634 (t80) cc_final: 0.7274 (t80) REVERT: F 263 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: F 357 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7105 (mmt) REVERT: F 422 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6882 (m-80) outliers start: 68 outliers final: 48 residues processed: 170 average time/residue: 0.3411 time to fit residues: 101.2627 Evaluate side-chains 155 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 96 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 242 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 232 optimal weight: 0.7980 chunk 276 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 346 optimal weight: 0.9980 chunk 322 optimal weight: 8.9990 chunk 176 optimal weight: 0.0070 chunk 89 optimal weight: 9.9990 chunk 300 optimal weight: 0.0270 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090405 restraints weight = 54544.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089385 restraints weight = 60933.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.090447 restraints weight = 67341.969| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 29422 Z= 0.113 Angle : 0.578 18.674 39804 Z= 0.289 Chirality : 0.042 0.460 4354 Planarity : 0.003 0.041 5106 Dihedral : 5.987 60.352 4210 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.11 % Allowed : 14.00 % Favored : 83.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % 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: 1.00 (0.14), residues: 3560 helix: 2.22 (0.13), residues: 1698 sheet: -0.63 (0.28), residues: 352 loop : -0.84 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 453 HIS 0.003 0.001 HIS C 598 PHE 0.014 0.001 PHE D 84 TYR 0.022 0.001 TYR F 525 ARG 0.004 0.000 ARG E 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00884 ( 10) link_NAG-ASN : angle 4.20174 ( 30) link_BETA1-4 : bond 0.00686 ( 6) link_BETA1-4 : angle 3.95389 ( 18) hydrogen bonds : bond 0.04981 ( 1414) hydrogen bonds : angle 4.20996 ( 4194) SS BOND : bond 0.00330 ( 46) SS BOND : angle 1.43337 ( 92) covalent geometry : bond 0.00223 (29360) covalent geometry : angle 0.55700 (39664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 115 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8023 (mtm) cc_final: 0.7685 (ttm) REVERT: B 126 ASP cc_start: 0.7489 (t70) cc_final: 0.7232 (t0) REVERT: B 679 MET cc_start: 0.8773 (mtt) cc_final: 0.8483 (mtm) REVERT: C 62 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8456 (pp) REVERT: C 112 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8793 (tm) REVERT: C 309 MET cc_start: 0.8506 (ttm) cc_final: 0.8245 (mtp) REVERT: C 499 MET cc_start: 0.8157 (ptm) cc_final: 0.7955 (ptm) REVERT: C 514 TYR cc_start: 0.8067 (m-10) cc_final: 0.7596 (m-80) REVERT: C 643 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7559 (p0) REVERT: D 62 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8521 (pp) REVERT: D 112 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8903 (tm) REVERT: D 309 MET cc_start: 0.8618 (ttm) cc_final: 0.8142 (mtp) REVERT: D 313 MET cc_start: 0.9012 (tpp) cc_final: 0.8603 (ttt) REVERT: D 354 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8357 (tttm) REVERT: D 499 MET cc_start: 0.8285 (ptm) cc_final: 0.7939 (ptm) REVERT: D 514 TYR cc_start: 0.8148 (m-10) cc_final: 0.7657 (m-80) REVERT: E 205 PHE cc_start: 0.7905 (t80) cc_final: 0.7496 (t80) REVERT: E 263 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: E 352 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8840 (mt) REVERT: E 632 LEU cc_start: 0.3484 (OUTLIER) cc_final: 0.3203 (tt) REVERT: F 205 PHE cc_start: 0.7465 (t80) cc_final: 0.7081 (t80) REVERT: F 263 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: F 357 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7104 (mmt) REVERT: F 422 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6761 (m-80) outliers start: 66 outliers final: 44 residues processed: 176 average time/residue: 0.3538 time to fit residues: 107.7420 Evaluate side-chains 156 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 63.2448 > 50: distance: 127 - 135: 19.218 distance: 135 - 136: 19.854 distance: 136 - 137: 11.737 distance: 137 - 138: 21.992 distance: 137 - 139: 7.457 distance: 139 - 140: 9.938 distance: 140 - 141: 21.655 distance: 140 - 143: 10.699 distance: 141 - 142: 34.221 distance: 141 - 148: 20.586 distance: 143 - 144: 17.798 distance: 144 - 145: 39.243 distance: 145 - 146: 34.015 distance: 146 - 147: 16.790 distance: 148 - 149: 26.679 distance: 149 - 150: 16.866 distance: 149 - 152: 16.767 distance: 150 - 156: 3.476 distance: 152 - 153: 42.279 distance: 153 - 154: 41.025 distance: 153 - 155: 26.796 distance: 156 - 157: 12.053 distance: 157 - 158: 17.283 distance: 157 - 160: 16.467 distance: 158 - 159: 34.467 distance: 158 - 164: 17.095 distance: 160 - 161: 20.829 distance: 161 - 162: 8.313 distance: 161 - 163: 43.461 distance: 164 - 165: 49.633 distance: 165 - 168: 41.545 distance: 166 - 167: 44.688 distance: 166 - 172: 44.881 distance: 168 - 169: 13.099 distance: 169 - 170: 24.766 distance: 169 - 171: 28.801 distance: 172 - 173: 31.204 distance: 173 - 174: 14.240 distance: 173 - 176: 16.874 distance: 174 - 175: 44.466 distance: 174 - 183: 22.620 distance: 176 - 177: 15.689 distance: 177 - 178: 16.768 distance: 177 - 179: 25.189 distance: 178 - 180: 28.686 distance: 179 - 181: 7.623 distance: 180 - 182: 31.513 distance: 181 - 182: 13.142 distance: 183 - 184: 14.668 distance: 184 - 185: 36.935 distance: 184 - 187: 44.165 distance: 185 - 186: 23.122 distance: 185 - 192: 8.883 distance: 187 - 188: 13.965 distance: 188 - 189: 25.789 distance: 189 - 190: 6.258 distance: 190 - 191: 26.593 distance: 192 - 193: 5.470 distance: 193 - 194: 30.608 distance: 193 - 196: 30.745 distance: 194 - 195: 49.405 distance: 194 - 200: 29.217 distance: 196 - 197: 19.399 distance: 197 - 198: 10.213 distance: 197 - 199: 34.186 distance: 200 - 201: 6.289 distance: 201 - 202: 29.944 distance: 201 - 204: 35.053 distance: 202 - 203: 5.454 distance: 202 - 206: 35.517 distance: 206 - 207: 21.679 distance: 207 - 208: 20.996 distance: 207 - 210: 14.850 distance: 208 - 209: 33.523 distance: 208 - 211: 16.953