Starting phenix.real_space_refine on Sun Sep 13 06:01:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3j94_6204/09_2026/3j94_6204.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j94_6204/09_2026/3j94_6204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2026/3j94_6204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2026/3j94_6204.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2026/3j94_6204.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2026/3j94_6204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2026/3j94_6204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2026/3j94_6204.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 93 5.16 5 C 13558 2.51 5 N 3719 2.21 5 O 4106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21509 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3559 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'CIS': 7, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 10, 'GLN:plan1': 3, 'ASN:plan1': 6, 'ASP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 166 Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3563 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 3, 'ASN:plan1': 6, 'GLU:plan': 8, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3573 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'CIS': 4, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 4, 'ASN:plan1': 6, 'GLU:plan': 8, 'PHE:plan': 3, 'ASP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3526 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 6, 'GLU:plan': 10, 'PHE:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 160 Chain: "E" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3529 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 454} Chain breaks: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 8, 'GLN:plan1': 3, 'ASN:plan1': 5, 'GLU:plan': 9, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 138 Chain: "F" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3418 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 18, 'TRANS': 439} Chain breaks: 2 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'GLU:plan': 10, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.24 Number of scatterers: 21509 At special positions: 0 Unit cell: (142.225, 137.363, 114.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 33 15.00 O 4106 8.00 N 3719 7.00 C 13558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "HETATM21258 O5' ATP B 801 .*. O " rejected from bonding due to valence issues. Atom "HETATM21475 O5' ATP E 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21289 O5' ATP B 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21351 O5' ATP C 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21413 O5' ATP D 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21413 O5' ATP D 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21258 O5' ATP B 801 .*. O " rejected from bonding due to valence issues. Atom "HETATM21503 O3B ATP F 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=40, symmetry=0 Number of additional bonds: simple=40, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 980.2 milliseconds 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5360 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 16 sheets defined 59.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 223 through 240 removed outlier: 4.099A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 removed outlier: 4.246A pdb=" N GLU A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.529A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.352A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 359 removed outlier: 3.732A pdb=" N ASN A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 399 through 417 removed outlier: 4.088A pdb=" N HIS A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 511 through 531 removed outlier: 4.124A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.891A pdb=" N ALA A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 577 through 595 Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 619 through 632 removed outlier: 3.846A pdb=" N LEU A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.575A pdb=" N LEU A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.956A pdb=" N ALA A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 661' Processing helix chain 'A' and resid 672 through 684 removed outlier: 3.778A pdb=" N LEU A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.622A pdb=" N GLN A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.974A pdb=" N GLN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.945A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.365A pdb=" N SER B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 removed outlier: 4.421A pdb=" N GLU B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 278 removed outlier: 3.683A pdb=" N LEU B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 317 removed outlier: 4.273A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 removed outlier: 4.098A pdb=" N ASN B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.234A pdb=" N LEU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 385' Processing helix chain 'B' and resid 399 through 417 removed outlier: 3.718A pdb=" N HIS B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 437 through 457 removed outlier: 3.506A pdb=" N LEU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 496 through 502 removed outlier: 4.224A pdb=" N ALA B 500 " --> pdb=" O GLN B 496 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 502 " --> pdb=" O ASP B 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 502' Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.930A pdb=" N THR B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.665A pdb=" N ASN B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.660A pdb=" N ILE B 574 " --> pdb=" O ASP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 removed outlier: 3.675A pdb=" N SER B 595 " --> pdb=" O ASP B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 619 through 632 removed outlier: 3.600A pdb=" N LEU B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 656 removed outlier: 4.190A pdb=" N LEU B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.951A pdb=" N ALA B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 661' Processing helix chain 'B' and resid 673 through 684 Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 707 through 719 Processing helix chain 'B' and resid 724 through 736 removed outlier: 3.685A pdb=" N GLU B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 240 removed outlier: 3.867A pdb=" N ALA C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 removed outlier: 4.425A pdb=" N GLU C 246 " --> pdb=" O PRO C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 278 removed outlier: 3.560A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.575A pdb=" N ASP C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 348 through 359 removed outlier: 3.954A pdb=" N ASN C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 355 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 357 " --> pdb=" O GLN C 353 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.945A pdb=" N LEU C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 417 removed outlier: 3.756A pdb=" N HIS C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 Processing helix chain 'C' and resid 437 through 457 removed outlier: 3.615A pdb=" N VAL C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 498 through 503 Processing helix chain 'C' and resid 511 through 531 removed outlier: 4.143A pdb=" N THR C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.800A pdb=" N ASN C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 595 Processing helix chain 'C' and resid 604 through 610 removed outlier: 3.799A pdb=" N ASP C 610 " --> pdb=" O GLU C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 632 removed outlier: 3.673A pdb=" N LEU C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 656 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.988A pdb=" N ALA C 660 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C 661 " --> pdb=" O MET C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 673 through 684 Processing helix chain 'C' and resid 687 through 699 removed outlier: 3.599A pdb=" N ARG C 691 " --> pdb=" O LYS C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 720 removed outlier: 3.522A pdb=" N GLN C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET C 720 " --> pdb=" O MET C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 737 removed outlier: 3.822A pdb=" N LYS C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 240 removed outlier: 3.631A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 removed outlier: 4.229A pdb=" N GLU D 246 " --> pdb=" O PRO D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 278 removed outlier: 3.731A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN D 278 " --> pdb=" O GLY D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 317 removed outlier: 3.935A pdb=" N PHE D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 380 through 385 removed outlier: 4.114A pdb=" N LEU D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 385 " --> pdb=" O GLU D 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 380 through 385' Processing helix chain 'D' and resid 399 through 417 removed outlier: 3.692A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 433 Processing helix chain 'D' and resid 437 through 457 removed outlier: 3.595A pdb=" N GLN D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 488 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 511 through 531 removed outlier: 3.588A pdb=" N THR D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 569 through 574 removed outlier: 3.589A pdb=" N MET D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 removed outlier: 3.700A pdb=" N CYS D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER D 595 " --> pdb=" O ASP D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 610 Processing helix chain 'D' and resid 619 through 632 Processing helix chain 'D' and resid 648 through 656 removed outlier: 3.861A pdb=" N LEU D 652 " --> pdb=" O ARG D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 removed outlier: 4.183A pdb=" N ALA D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE D 661 " --> pdb=" O MET D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 661' Processing helix chain 'D' and resid 673 through 684 Processing helix chain 'D' and resid 687 through 699 Processing helix chain 'D' and resid 706 through 718 Processing helix chain 'D' and resid 724 through 736 removed outlier: 3.907A pdb=" N LYS D 728 " --> pdb=" O TYR D 724 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 729 " --> pdb=" O ARG D 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 240 removed outlier: 4.320A pdb=" N SER E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 249 removed outlier: 4.507A pdb=" N GLU E 246 " --> pdb=" O PRO E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 278 removed outlier: 3.680A pdb=" N LEU E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN E 278 " --> pdb=" O GLY E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 317 removed outlier: 4.178A pdb=" N PHE E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 359 removed outlier: 4.281A pdb=" N ASN E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 385 removed outlier: 3.993A pdb=" N LEU E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG E 385 " --> pdb=" O GLU E 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 380 through 385' Processing helix chain 'E' and resid 399 through 417 removed outlier: 3.682A pdb=" N HIS E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS E 417 " --> pdb=" O ARG E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 437 through 457 removed outlier: 3.772A pdb=" N LEU E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 488 Processing helix chain 'E' and resid 511 through 530 removed outlier: 4.235A pdb=" N ASN E 530 " --> pdb=" O GLN E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 561 Processing helix chain 'E' and resid 569 through 574 removed outlier: 3.828A pdb=" N MET E 573 " --> pdb=" O SER E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 594 removed outlier: 3.547A pdb=" N TYR E 593 " --> pdb=" O PHE E 589 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 619 through 632 removed outlier: 3.816A pdb=" N LEU E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 655 removed outlier: 4.038A pdb=" N LEU E 652 " --> pdb=" O ARG E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 661 Processing helix chain 'E' and resid 672 through 684 Processing helix chain 'E' and resid 687 through 699 removed outlier: 3.992A pdb=" N LYS E 699 " --> pdb=" O ALA E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 719 removed outlier: 3.767A pdb=" N GLN E 719 " --> pdb=" O GLU E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 737 removed outlier: 4.292A pdb=" N VAL E 726 " --> pdb=" O PRO E 722 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG E 727 " --> pdb=" O GLU E 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 240 removed outlier: 4.212A pdb=" N SER F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.685A pdb=" N LEU F 269 " --> pdb=" O GLY F 265 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN F 278 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 317 removed outlier: 4.025A pdb=" N PHE F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 359 removed outlier: 4.082A pdb=" N ASN F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 417 removed outlier: 3.905A pdb=" N ARG F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 removed outlier: 3.722A pdb=" N THR F 433 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 457 removed outlier: 3.719A pdb=" N LEU F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU F 442 " --> pdb=" O GLY F 438 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 457 " --> pdb=" O MET F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 503 removed outlier: 4.087A pdb=" N TYR F 502 " --> pdb=" O ASP F 498 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 503 " --> pdb=" O TYR F 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 498 through 503' Processing helix chain 'F' and resid 511 through 531 removed outlier: 3.703A pdb=" N LEU F 518 " --> pdb=" O VAL F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 561 removed outlier: 3.871A pdb=" N ASN F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 574 Processing helix chain 'F' and resid 577 through 595 removed outlier: 3.931A pdb=" N SER F 595 " --> pdb=" O ASP F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 610 Processing helix chain 'F' and resid 619 through 632 removed outlier: 3.514A pdb=" N LEU F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 655 Processing helix chain 'F' and resid 656 through 661 removed outlier: 4.060A pdb=" N ALA F 660 " --> pdb=" O GLU F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 684 Processing helix chain 'F' and resid 687 through 699 Processing helix chain 'F' and resid 706 through 719 removed outlier: 3.627A pdb=" N LEU F 710 " --> pdb=" O GLY F 706 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN F 719 " --> pdb=" O GLU F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 736 removed outlier: 4.734A pdb=" N ARG F 727 " --> pdb=" O GLU F 723 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 284 through 285 removed outlier: 5.308A pdb=" N VAL A 284 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP A 328 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N HIS A 323 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 370 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 391 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.095A pdb=" N PHE A 564 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 601 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS A 566 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR A 663 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER A 538 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE A 665 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 540 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 284 through 286 removed outlier: 6.722A pdb=" N VAL B 284 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP B 328 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN B 286 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HIS B 323 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE B 370 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE B 325 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N MET B 372 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE B 327 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 371 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 373 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY B 255 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N MET B 393 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 257 " --> pdb=" O MET B 393 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 564 through 568 removed outlier: 6.273A pdb=" N PHE B 564 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 601 " --> pdb=" O PHE B 564 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS B 566 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 537 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLY B 644 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 539 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR B 646 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B 541 " --> pdb=" O THR B 646 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR B 663 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER B 538 " --> pdb=" O THR B 663 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE B 665 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 540 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 670 through 672 removed outlier: 4.751A pdb=" N THR B 672 " --> pdb=" O VAL B 703 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL B 703 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'C' and resid 284 through 286 removed outlier: 6.483A pdb=" N VAL C 284 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASP C 328 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN C 286 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS C 323 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE C 370 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 325 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N MET C 372 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE C 327 " --> pdb=" O MET C 372 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 371 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 373 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY C 255 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N MET C 393 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C 257 " --> pdb=" O MET C 393 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 564 through 568 removed outlier: 4.448A pdb=" N PHE C 564 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS C 599 " --> pdb=" O PHE C 564 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 670 through 672 removed outlier: 4.753A pdb=" N THR C 672 " --> pdb=" O VAL C 703 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 703 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'D' and resid 284 through 286 removed outlier: 5.972A pdb=" N VAL D 284 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET D 372 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR D 373 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY D 255 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N MET D 393 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 257 " --> pdb=" O MET D 393 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 564 through 568 removed outlier: 3.782A pdb=" N PHE D 564 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 537 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY D 644 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL D 539 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N THR D 663 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER D 538 " --> pdb=" O THR D 663 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE D 665 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU D 540 " --> pdb=" O ILE D 665 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'D' and resid 670 through 672 removed outlier: 4.609A pdb=" N ALA D 671 " --> pdb=" O VAL D 703 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'E' and resid 284 through 285 removed outlier: 6.583A pdb=" N VAL E 284 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASP E 328 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 368 " --> pdb=" O HIS E 323 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY E 371 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 373 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY E 255 " --> pdb=" O VAL E 391 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N MET E 393 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU E 257 " --> pdb=" O MET E 393 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'E' and resid 564 through 566 removed outlier: 6.835A pdb=" N PHE E 564 " --> pdb=" O CYS E 599 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL E 601 " --> pdb=" O PHE E 564 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS E 566 " --> pdb=" O VAL E 601 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'F' and resid 284 through 286 removed outlier: 6.405A pdb=" N VAL F 284 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP F 328 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN F 286 " --> pdb=" O ASP F 328 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N HIS F 323 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE F 370 " --> pdb=" O HIS F 323 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE F 325 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N MET F 372 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE F 327 " --> pdb=" O MET F 372 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU F 258 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU F 257 " --> pdb=" O MET F 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=N Processing sheet with id=O, first strand: chain 'F' and resid 564 through 568 removed outlier: 4.236A pdb=" N PHE F 564 " --> pdb=" O LEU F 597 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL F 537 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 540 " --> pdb=" O THR F 663 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'F' and resid 670 through 672 removed outlier: 3.995A pdb=" N ALA F 671 " --> pdb=" O VAL F 703 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3851 1.32 - 1.45: 4837 1.45 - 1.57: 12892 1.57 - 1.69: 103 1.69 - 1.82: 156 Bond restraints: 21839 Sorted by residual: bond pdb=" C5 ATP E 801 " pdb=" C6 ATP E 801 " ideal model delta sigma weight residual 1.409 1.517 -0.108 1.00e-02 1.00e+04 1.17e+02 bond pdb=" C4 ATP B 802 " pdb=" C5 ATP B 802 " ideal model delta sigma weight residual 1.388 1.482 -0.094 1.00e-02 1.00e+04 8.84e+01 bond pdb=" C4 ATP C 802 " pdb=" C5 ATP C 802 " ideal model delta sigma weight residual 1.388 1.482 -0.094 1.00e-02 1.00e+04 8.76e+01 bond pdb=" C5 ATP D 802 " pdb=" C6 ATP D 802 " ideal model delta sigma weight residual 1.409 1.501 -0.092 1.00e-02 1.00e+04 8.42e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.496 -0.087 1.00e-02 1.00e+04 7.59e+01 ... (remaining 21834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 28527 4.50 - 9.01: 1066 9.01 - 13.51: 79 13.51 - 18.02: 13 18.02 - 22.52: 11 Bond angle restraints: 29696 Sorted by residual: angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 117.35 22.52 1.00e+00 1.00e+00 5.07e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 119.20 20.67 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 119.45 20.42 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PA ATP F 801 " pdb=" O3A ATP F 801 " pdb=" PB ATP F 801 " ideal model delta sigma weight residual 136.83 116.42 20.41 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 119.52 20.35 1.00e+00 1.00e+00 4.14e+02 ... (remaining 29691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11824 17.98 - 35.95: 952 35.95 - 53.93: 287 53.93 - 71.90: 80 71.90 - 89.88: 34 Dihedral angle restraints: 13177 sinusoidal: 4901 harmonic: 8276 Sorted by residual: dihedral pdb=" CA PRO A 261 " pdb=" C PRO A 261 " pdb=" N PRO A 262 " pdb=" CA PRO A 262 " ideal model delta harmonic sigma weight residual 180.00 135.63 44.37 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA GLY B 438 " pdb=" C GLY B 438 " pdb=" N ALA B 439 " pdb=" CA ALA B 439 " ideal model delta harmonic sigma weight residual 180.00 142.87 37.13 0 5.00e+00 4.00e-02 5.51e+01 dihedral pdb=" CA GLY F 438 " pdb=" C GLY F 438 " pdb=" N ALA F 439 " pdb=" CA ALA F 439 " ideal model delta harmonic sigma weight residual 180.00 143.61 36.39 0 5.00e+00 4.00e-02 5.30e+01 ... (remaining 13174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3020 0.101 - 0.203: 446 0.203 - 0.304: 55 0.304 - 0.405: 4 0.405 - 0.507: 5 Chirality restraints: 3530 Sorted by residual: chirality pdb=" CB VAL A 525 " pdb=" CA VAL A 525 " pdb=" CG1 VAL A 525 " pdb=" CG2 VAL A 525 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CB ILE E 670 " pdb=" CA ILE E 670 " pdb=" CG1 ILE E 670 " pdb=" CG2 ILE E 670 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CG LEU A 444 " pdb=" CB LEU A 444 " pdb=" CD1 LEU A 444 " pdb=" CD2 LEU A 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 3527 not shown) Planarity restraints: 3801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 530 " -0.046 2.00e-02 2.50e+03 9.01e-02 8.11e+01 pdb=" CG ASN C 530 " 0.156 2.00e-02 2.50e+03 pdb=" OD1 ASN C 530 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN C 530 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 596 " -0.042 2.00e-02 2.50e+03 8.31e-02 6.90e+01 pdb=" CD GLN D 596 " 0.144 2.00e-02 2.50e+03 pdb=" OE1 GLN D 596 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 GLN D 596 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 546 " 0.077 2.00e-02 2.50e+03 6.17e-02 5.70e+01 pdb=" CG HIS B 546 " -0.121 2.00e-02 2.50e+03 pdb=" ND1 HIS B 546 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 546 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS B 546 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS B 546 " 0.040 2.00e-02 2.50e+03 ... (remaining 3798 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 16 1.99 - 2.72: 1483 2.72 - 3.44: 34548 3.44 - 4.17: 48583 4.17 - 4.90: 83561 Nonbonded interactions: 168191 Sorted by model distance: nonbonded pdb=" OE1 GLU E 442 " pdb=" O2' ATP E 802 " model vdw 1.261 3.040 nonbonded pdb=" O SER F 547 " pdb=" O2B ATP F 801 " model vdw 1.263 3.040 nonbonded pdb=" OG1 THR F 550 " pdb=" O1B ATP F 801 " model vdw 1.264 3.040 nonbonded pdb=" OE1 GLU B 442 " pdb=" O2' ATP B 802 " model vdw 1.264 3.040 nonbonded pdb=" OG1 THR D 267 " pdb=" O2B ATP D 802 " model vdw 1.264 3.040 ... (remaining 168186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 230 or (resid 231 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 267 or (resid 268 through 270 and (name N or name CA or name C \ or name O or name CB )) or resid 271 through 293 or (resid 294 through 295 and \ (name N or name CA or name C or name O or name CB )) or resid 296 through 302 or \ (resid 303 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 4 through 305 or (resid 306 through 307 and (name N or name CA or name C or name \ O or name CB )) or resid 308 through 314 or (resid 315 and (name N or name CA o \ r name C or name O or name CB )) or resid 316 through 321 or (resid 322 and (nam \ e N or name CA or name C or name O or name CB )) or resid 323 through 324 or (re \ sid 325 and (name N or name CA or name C or name O or name CB )) or resid 326 th \ rough 329 or (resid 330 and (name N or name CA or name C or name O or name CB )) \ or resid 348 through 351 or (resid 352 through 353 and (name N or name CA or na \ me C or name O or name CB )) or resid 354 through 356 or (resid 357 through 359 \ and (name N or name CA or name C or name O or name CB )) or resid 360 through 38 \ 2 or (resid 383 and (name N or name CA or name C or name O or name CB )) or resi \ d 384 through 396 or (resid 397 and (name N or name CA or name C or name O or na \ me CB )) or resid 398 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB )) or resid 408 through 413 or (resid 414 through 415 and \ (name N or name CA or name C or name O or name CB )) or resid 416 through 418 or \ (resid 419 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 0 through 423 or (resid 424 and (name N or name CA or name C or name O or name C \ B )) or resid 425 through 435 or (resid 436 and (name N or name CA or name C or \ name O or name CB )) or resid 437 through 441 or (resid 442 and (name N or name \ CA or name C or name O or name CB )) or resid 443 or (resid 444 and (name N or n \ ame CA or name C or name O or name CB )) or resid 445 or (resid 446 through 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 through 45 \ 7 or (resid 497 and (name N or name CA or name C or name O or name CB )) or resi \ d 498 or (resid 499 through 500 and (name N or name CA or name C or name O or na \ me CB )) or resid 501 through 507 or (resid 508 and (name N or name CA or name C \ or name O or name CB )) or resid 509 through 523 or (resid 524 and (name N or n \ ame CA or name C or name O or name CB )) or resid 525 through 532 or (resid 533 \ and (name N or name CA or name C or name O or name CB )) or resid 534 through 54 \ 1 or (resid 542 and (name N or name CA or name C or name O or name CB )) or resi \ d 543 through 565 or (resid 566 and (name N or name CA or name C or name O or na \ me CB )) or resid 567 through 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 630 through 635 or (resid 636 and (name N or n \ ame CA or name C or name O or name CB )) or resid 637 through 650 or (resid 651 \ and (name N or name CA or name C or name O or name CB )) or resid 652 through 65 \ 5 or (resid 656 and (name N or name CA or name C or name O or name CB )) or resi \ d 657 through 673 or (resid 674 and (name N or name CA or name C or name O or na \ me CB )) or resid 675 through 690 or (resid 691 and (name N or name CA or name C \ or name O or name CB )) or resid 692 through 701 or (resid 702 and (name N or n \ ame CA or name C or name O or name CB )) or resid 703 through 717 or (resid 718 \ and (name N or name CA or name C or name O or name CB )) or resid 719 through 80 \ 1)) selection = (chain 'B' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 230 or (resid 231 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 265 or (resid 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 or (resid 268 through 270 and (name N or name CA or na \ me C or name O or name CB )) or resid 271 through 293 or (resid 294 through 295 \ and (name N or name CA or name C or name O or name CB )) or resid 296 through 30 \ 2 or (resid 303 and (name N or name CA or name C or name O or name CB )) or resi \ d 304 through 305 or (resid 306 through 307 and (name N or name CA or name C or \ name O or name CB )) or resid 308 through 311 or (resid 312 and (name N or name \ CA or name C or name O or name CB )) or resid 313 or (resid 314 through 315 and \ (name N or name CA or name C or name O or name CB )) or resid 316 through 321 or \ (resid 322 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 3 through 324 or (resid 325 and (name N or name CA or name C or name O or name C \ B )) or resid 326 through 329 or (resid 330 and (name N or name CA or name C or \ name O or name CB )) or resid 348 through 351 or (resid 352 through 353 and (nam \ e N or name CA or name C or name O or name CB )) or resid 354 through 356 or (re \ sid 357 through 359 and (name N or name CA or name C or name O or name CB )) or \ resid 360 through 371 or (resid 372 through 373 and (name N or name CA or name C \ or name O or name CB )) or resid 374 through 382 or (resid 383 and (name N or n \ ame CA or name C or name O or name CB )) or resid 384 or (resid 385 and (name N \ or name CA or name C or name O or name CB )) or resid 386 through 387 or (resid \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 throug \ h 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or \ resid 398 through 406 or (resid 407 and (name N or name CA or name C or name O o \ r name CB )) or resid 408 through 412 or (resid 413 through 415 and (name N or n \ ame CA or name C or name O or name CB )) or resid 416 through 418 or (resid 419 \ and (name N or name CA or name C or name O or name CB )) or resid 420 through 42 \ 3 or (resid 424 and (name N or name CA or name C or name O or name CB )) or resi \ d 425 through 435 or (resid 436 and (name N or name CA or name C or name O or na \ me CB )) or resid 437 through 441 or (resid 442 and (name N or name CA or name C \ or name O or name CB )) or resid 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 454 or (resid 455 and (name N \ or name CA or name C or name O or name CB )) or resid 456 through 457 or (resid \ 497 and (name N or name CA or name C or name O or name CB )) or resid 498 throug \ h 523 or (resid 524 and (name N or name CA or name C or name O or name CB )) or \ resid 525 through 541 or (resid 542 and (name N or name CA or name C or name O o \ r name CB )) or resid 543 through 557 or (resid 558 and (name N or name CA or na \ me C or name O or name CB )) or resid 559 through 565 or (resid 566 and (name N \ or name CA or name C or name O or name CB )) or resid 567 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 throug \ h 628 or (resid 629 and (name N or name CA or name C or name O or name CB )) or \ resid 630 through 635 or (resid 636 and (name N or name CA or name C or name O o \ r name CB )) or resid 637 through 648 or (resid 649 and (name N or name CA or na \ me C or name O or name CB )) or resid 650 through 655 or (resid 656 and (name N \ or name CA or name C or name O or name CB )) or resid 657 through 673 or (resid \ 674 and (name N or name CA or name C or name O or name CB )) or resid 675 throug \ h 690 or (resid 691 and (name N or name CA or name C or name O or name CB )) or \ resid 692 through 701 or (resid 702 and (name N or name CA or name C or name O o \ r name CB )) or resid 703 through 714 or (resid 715 and (name N or name CA or na \ me C or name O or name CB )) or resid 716 through 717 or (resid 718 and (name N \ or name CA or name C or name O or name CB )) or resid 719 through 801)) selection = (chain 'C' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 230 or (resid 231 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 265 or (resid 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 through 268 or (resid 269 through 270 and (name N or n \ ame CA or name C or name O or name CB )) or resid 271 through 293 or (resid 294 \ through 295 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 6 through 311 or (resid 312 and (name N or name CA or name C or name O or name C \ B )) or resid 313 or (resid 314 through 315 and (name N or name CA or name C or \ name O or name CB )) or resid 316 through 321 or (resid 322 and (name N or name \ CA or name C or name O or name CB )) or resid 323 through 324 or (resid 325 and \ (name N or name CA or name C or name O or name CB )) or resid 326 through 330 or \ resid 348 through 351 or (resid 352 through 353 and (name N or name CA or name \ C or name O or name CB )) or resid 354 through 356 or (resid 357 through 359 and \ (name N or name CA or name C or name O or name CB )) or resid 360 through 372 o \ r (resid 373 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 74 through 382 or (resid 383 and (name N or name CA or name C or name O or name \ CB )) or resid 384 or (resid 385 and (name N or name CA or name C or name O or n \ ame CB )) or resid 386 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 396 or (resid 397 and (name N or \ name CA or name C or name O or name CB )) or resid 398 through 406 or (resid 407 \ and (name N or name CA or name C or name O or name CB )) or resid 408 through 4 \ 12 or (resid 413 through 415 and (name N or name CA or name C or name O or name \ CB )) or resid 416 through 418 or (resid 419 and (name N or name CA or name C or \ name O or name CB )) or resid 420 through 423 or (resid 424 and (name N or name \ CA or name C or name O or name CB )) or resid 425 through 435 or (resid 436 and \ (name N or name CA or name C or name O or name CB )) or resid 437 through 441 o \ r (resid 442 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 43 or (resid 444 and (name N or name CA or name C or name O or name CB )) or res \ id 445 through 454 or (resid 455 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 457 or (resid 497 and (name N or name CA or name \ C or name O or name CB )) or resid 498 or (resid 499 through 500 and (name N or \ name CA or name C or name O or name CB )) or resid 501 through 507 or (resid 508 \ and (name N or name CA or name C or name O or name CB )) or resid 509 through 5 \ 23 or (resid 524 and (name N or name CA or name C or name O or name CB )) or res \ id 525 through 532 or (resid 533 and (name N or name CA or name C or name O or n \ ame CB )) or resid 534 through 541 or (resid 542 and (name N or name CA or name \ C or name O or name CB )) or resid 543 through 557 or (resid 558 and (name N or \ name CA or name C or name O or name CB )) or resid 559 through 565 or (resid 566 \ and (name N or name CA or name C or name O or name CB )) or resid 567 through 5 \ 96 or (resid 597 and (name N or name CA or name C or name O or name CB )) or res \ id 598 through 628 or (resid 629 and (name N or name CA or name C or name O or n \ ame CB )) or resid 630 through 635 or (resid 636 and (name N or name CA or name \ C or name O or name CB )) or resid 637 through 648 or (resid 649 and (name N or \ name CA or name C or name O or name CB )) or resid 650 or (resid 651 and (name N \ or name CA or name C or name O or name CB )) or resid 652 through 655 or (resid \ 656 and (name N or name CA or name C or name O or name CB )) or resid 657 throu \ gh 673 or (resid 674 and (name N or name CA or name C or name O or name CB )) or \ resid 675 through 690 or (resid 691 and (name N or name CA or name C or name O \ or name CB )) or resid 692 through 701 or (resid 702 and (name N or name CA or n \ ame C or name O or name CB )) or resid 703 through 714 or (resid 715 and (name N \ or name CA or name C or name O or name CB )) or resid 716 through 717 or (resid \ 718 and (name N or name CA or name C or name O or name CB )) or resid 719 throu \ gh 801)) selection = (chain 'D' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 through 230 or (resid 231 through 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 26 \ 5 or (resid 266 and (name N or name CA or name C or name O or name CB )) or resi \ d 267 or (resid 268 through 270 and (name N or name CA or name C or name O or na \ me CB )) or resid 271 through 275 or (resid 276 through 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 293 or (resid 294 thro \ ugh 295 and (name N or name CA or name C or name O or name CB )) or resid 296 th \ rough 302 or (resid 303 and (name N or name CA or name C or name O or name CB )) \ or resid 304 through 311 or (resid 312 and (name N or name CA or name C or name \ O or name CB )) or resid 313 through 321 or (resid 322 and (name N or name CA o \ r name C or name O or name CB )) or resid 323 through 324 or (resid 325 and (nam \ e N or name CA or name C or name O or name CB )) or resid 326 through 329 or (re \ sid 330 and (name N or name CA or name C or name O or name CB )) or resid 348 th \ rough 351 or (resid 352 through 353 and (name N or name CA or name C or name O o \ r name CB )) or resid 354 through 357 or (resid 358 through 359 and (name N or n \ ame CA or name C or name O or name CB )) or resid 360 through 371 or (resid 372 \ through 373 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 4 through 382 or (resid 383 and (name N or name CA or name C or name O or name C \ B )) or resid 384 through 387 or (resid 388 and (name N or name CA or name C or \ name O or name CB )) or resid 389 through 406 or (resid 407 and (name N or name \ CA or name C or name O or name CB )) or resid 408 through 412 or (resid 413 thro \ ugh 415 and (name N or name CA or name C or name O or name CB )) or resid 416 th \ rough 418 or (resid 419 and (name N or name CA or name C or name O or name CB )) \ or resid 420 through 423 or (resid 424 and (name N or name CA or name C or name \ O or name CB )) or resid 425 through 435 or (resid 436 and (name N or name CA o \ r name C or name O or name CB )) or resid 437 through 443 or (resid 444 and (nam \ e N or name CA or name C or name O or name CB )) or resid 445 through 457 or res \ id 497 through 498 or (resid 499 through 500 and (name N or name CA or name C or \ name O or name CB )) or resid 501 through 507 or (resid 508 and (name N or name \ CA or name C or name O or name CB )) or resid 509 through 523 or (resid 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 532 o \ r (resid 533 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 34 through 541 or (resid 542 and (name N or name CA or name C or name O or name \ CB )) or resid 543 through 557 or (resid 558 and (name N or name CA or name C or \ name O or name CB )) or resid 559 through 565 or (resid 566 and (name N or name \ CA or name C or name O or name CB )) or resid 567 through 596 or (resid 597 and \ (name N or name CA or name C or name O or name CB )) or resid 598 through 628 o \ r (resid 629 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 30 through 635 or (resid 636 and (name N or name CA or name C or name O or name \ CB )) or resid 637 through 648 or (resid 649 and (name N or name CA or name C or \ name O or name CB )) or resid 650 or (resid 651 and (name N or name CA or name \ C or name O or name CB )) or resid 652 through 655 or (resid 656 and (name N or \ name CA or name C or name O or name CB )) or resid 657 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 through 6 \ 90 or (resid 691 and (name N or name CA or name C or name O or name CB )) or res \ id 692 through 701 or (resid 702 and (name N or name CA or name C or name O or n \ ame CB )) or resid 703 through 714 or (resid 715 and (name N or name CA or name \ C or name O or name CB )) or resid 716 through 717 or (resid 718 and (name N or \ name CA or name C or name O or name CB )) or resid 719 through 801)) selection = (chain 'E' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 231 or (resid 232 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 265 or (resid 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 or (resid 268 through 270 and (name N or name CA or na \ me C or name O or name CB )) or resid 271 through 293 or (resid 294 through 295 \ and (name N or name CA or name C or name O or name CB )) or resid 296 through 30 \ 2 or (resid 303 and (name N or name CA or name C or name O or name CB )) or resi \ d 304 through 305 or (resid 306 through 307 and (name N or name CA or name C or \ name O or name CB )) or resid 308 through 311 or (resid 312 and (name N or name \ CA or name C or name O or name CB )) or resid 313 or (resid 314 through 315 and \ (name N or name CA or name C or name O or name CB )) or resid 316 through 324 or \ (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 6 through 329 or (resid 330 and (name N or name CA or name C or name O or name C \ B )) or resid 348 through 351 or (resid 352 through 353 and (name N or name CA o \ r name C or name O or name CB )) or resid 354 through 356 or (resid 357 through \ 359 and (name N or name CA or name C or name O or name CB )) or resid 360 throug \ h 371 or (resid 372 through 373 and (name N or name CA or name C or name O or na \ me CB )) or resid 374 through 382 or (resid 383 and (name N or name CA or name C \ or name O or name CB )) or resid 384 through 387 or (resid 388 and (name N or n \ ame CA or name C or name O or name CB )) or resid 389 through 396 or (resid 397 \ and (name N or name CA or name C or name O or name CB )) or resid 398 through 41 \ 8 or (resid 419 and (name N or name CA or name C or name O or name CB )) or resi \ d 420 through 423 or (resid 424 and (name N or name CA or name C or name O or na \ me CB )) or resid 425 through 435 or (resid 436 and (name N or name CA or name C \ or name O or name CB )) or resid 437 through 441 or (resid 442 and (name N or n \ ame CA or name C or name O or name CB )) or resid 443 or (resid 444 and (name N \ or name CA or name C or name O or name CB )) or resid 445 through 454 or (resid \ 455 and (name N or name CA or name C or name O or name CB )) or resid 456 throug \ h 457 or (resid 497 and (name N or name CA or name C or name O or name CB )) or \ resid 498 or (resid 499 through 500 and (name N or name CA or name C or name O o \ r name CB )) or resid 501 through 507 or (resid 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 523 or (resid 524 and (name N \ or name CA or name C or name O or name CB )) or resid 525 through 532 or (resid \ 533 and (name N or name CA or name C or name O or name CB )) or resid 534 throug \ h 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) or \ resid 559 through 596 or (resid 597 and (name N or name CA or name C or name O o \ r name CB )) or resid 598 through 648 or (resid 649 and (name N or name CA or na \ me C or name O or name CB )) or resid 650 or (resid 651 and (name N or name CA o \ r name C or name O or name CB )) or resid 652 through 655 or (resid 656 and (nam \ e N or name CA or name C or name O or name CB )) or resid 657 through 673 or (re \ sid 674 and (name N or name CA or name C or name O or name CB )) or resid 675 th \ rough 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) \ or resid 703 through 714 or (resid 715 and (name N or name CA or name C or name \ O or name CB )) or resid 716 through 717 or (resid 718 and (name N or name CA o \ r name C or name O or name CB )) or resid 719 through 801)) selection = (chain 'F' and (resid 217 through 224 or (resid 225 and (name N or name CA or na \ me C or name O or name CB )) or resid 226 through 230 or (resid 231 through 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 26 \ 7 or (resid 268 through 270 and (name N or name CA or name C or name O or name C \ B )) or resid 271 through 302 or (resid 303 and (name N or name CA or name C or \ name O or name CB )) or resid 304 through 305 or (resid 306 through 307 and (nam \ e N or name CA or name C or name O or name CB )) or resid 308 through 311 or (re \ sid 312 and (name N or name CA or name C or name O or name CB )) or resid 313 or \ (resid 314 through 315 and (name N or name CA or name C or name O or name CB )) \ or resid 316 through 321 or (resid 322 and (name N or name CA or name C or name \ O or name CB )) or resid 323 through 329 or (resid 330 and (name N or name CA o \ r name C or name O or name CB )) or resid 348 through 352 or (resid 353 and (nam \ e N or name CA or name C or name O or name CB )) or resid 354 through 356 or (re \ sid 357 through 359 and (name N or name CA or name C or name O or name CB )) or \ resid 360 through 371 or (resid 372 through 373 and (name N or name CA or name C \ or name O or name CB )) or resid 374 through 384 or (resid 385 and (name N or n \ ame CA or name C or name O or name CB )) or resid 386 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 39 \ 6 or (resid 397 and (name N or name CA or name C or name O or name CB )) or resi \ d 398 through 412 or (resid 413 through 415 and (name N or name CA or name C or \ name O or name CB )) or resid 416 through 445 or (resid 446 through 448 and (nam \ e N or name CA or name C or name O or name CB )) or resid 449 through 457 or (re \ sid 497 and (name N or name CA or name C or name O or name CB )) or resid 498 or \ (resid 499 through 500 and (name N or name CA or name C or name O or name CB )) \ or resid 501 through 507 or (resid 508 and (name N or name CA or name C or name \ O or name CB )) or resid 509 through 541 or (resid 542 and (name N or name CA o \ r name C or name O or name CB )) or resid 543 through 557 or (resid 558 and (nam \ e N or name CA or name C or name O or name CB )) or resid 559 through 565 or (re \ sid 566 and (name N or name CA or name C or name O or name CB )) or resid 567 th \ rough 596 or (resid 597 and (name N or name CA or name C or name O or name CB )) \ or resid 598 through 628 or (resid 629 and (name N or name CA or name C or name \ O or name CB )) or resid 630 through 635 or (resid 636 and (name N or name CA o \ r name C or name O or name CB )) or resid 637 through 648 or (resid 649 and (nam \ e N or name CA or name C or name O or name CB )) or resid 650 or (resid 651 and \ (name N or name CA or name C or name O or name CB )) or resid 652 through 690 or \ (resid 691 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 2 through 714 or (resid 715 and (name N or name CA or name C or name O or name C \ B )) or resid 716 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.420 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.013 0.863 21879 Z= 1.095 Angle : 1.965 22.523 29696 Z= 1.392 Chirality : 0.074 0.507 3530 Planarity : 0.006 0.090 3801 Dihedral : 15.844 89.875 7817 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 31.38 Ramachandran Plot: Outliers : 1.96 % Allowed : 5.01 % Favored : 93.03 % Rotamer: Outliers : 5.87 % Allowed : 21.59 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 1.53 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.16), residues: 2857 helix: 2.50 (0.13), residues: 1485 sheet: 3.34 (0.25), residues: 357 loop : -0.73 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG C 691 TYR 0.066 0.003 TYR F 259 PHE 0.046 0.004 PHE E 436 TRP 0.042 0.004 TRP E 510 HIS 0.056 0.004 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.63 (21839) covalent geometry : angle 1.96512 / 1.39 (29696) hydrogen bonds : bond 0.18805 / 13.20 ( 1139) hydrogen bonds : angle 7.65339 / 5.60 ( 3381) Misc. bond : bond 0.20974 / 15.14 ( 40) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 376 time to evaluate : 0.834 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: 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: 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: symmetry clash REVERT: A 418 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: A 552 LEU cc_start: 0.9511 (tt) cc_final: 0.9142 (mt) REVERT: A 573 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6738 (mmt) REVERT: A 602 VAL cc_start: 0.9244 (t) cc_final: 0.8951 (m) REVERT: B 378 LEU cc_start: 0.6746 (mt) cc_final: 0.6487 (mt) REVERT: B 573 MET cc_start: 0.8296 (mtt) cc_final: 0.7840 (mtt) REVERT: B 640 LEU cc_start: 0.7600 (tt) cc_final: 0.7388 (tp) REVERT: C 316 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8678 (tp) REVERT: C 426 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8933 (pp) REVERT: C 509 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8520 (tptp) REVERT: C 552 LEU cc_start: 0.9450 (mt) cc_final: 0.9231 (mt) REVERT: C 573 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7529 (mpp) REVERT: C 579 THR cc_start: 0.8804 (t) cc_final: 0.8587 (p) REVERT: C 587 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8882 (ttpp) REVERT: C 642 ILE cc_start: 0.9066 (mt) cc_final: 0.8850 (mp) REVERT: C 709 LYS cc_start: 0.9420 (tptm) cc_final: 0.9142 (tppt) REVERT: C 720 MET cc_start: 0.8637 (mmm) cc_final: 0.8432 (mtp) REVERT: D 305 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8765 (mm) REVERT: D 404 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8987 (mt) REVERT: D 586 LYS cc_start: 0.9286 (mtpt) cc_final: 0.8765 (mttm) REVERT: E 354 LEU cc_start: 0.9084 (mt) cc_final: 0.8793 (pp) REVERT: E 552 LEU cc_start: 0.9018 (mt) cc_final: 0.8757 (mt) REVERT: E 586 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8418 (pttm) REVERT: F 526 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.9023 (tp-100) REVERT: F 601 VAL cc_start: 0.8971 (t) cc_final: 0.8726 (t) REVERT: F 724 TYR cc_start: 0.9069 (m-80) cc_final: 0.8207 (m-10) outliers start: 123 outliers final: 26 residues processed: 479 average time/residue: 0.1630 time to fit residues: 116.8779 Evaluate side-chains 255 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.1980 chunk 111 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A 530 ASN B 286 ASN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN B 527 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN D 526 GLN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS E 697 GLN F 286 ASN F 526 GLN F 530 ASN F 620 ASN ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 697 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.044886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033025 restraints weight = 184283.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033704 restraints weight = 137598.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034246 restraints weight = 109004.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034682 restraints weight = 90341.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035022 restraints weight = 77164.012| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21879 Z= 0.216 Angle : 0.901 13.085 29696 Z= 0.466 Chirality : 0.047 0.415 3530 Planarity : 0.006 0.079 3801 Dihedral : 7.833 88.321 3056 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.84 % Allowed : 3.71 % Favored : 95.45 % Rotamer: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.15), residues: 2857 helix: 1.34 (0.12), residues: 1527 sheet: 2.73 (0.25), residues: 364 loop : -0.99 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 388 TYR 0.018 0.002 TYR D 611 PHE 0.048 0.003 PHE A 231 TRP 0.020 0.002 TRP A 510 HIS 0.012 0.002 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (21839) covalent geometry : angle 0.90064 / 0.47 (29696) hydrogen bonds : bond 0.05573 / 3.86 ( 1139) hydrogen bonds : angle 5.81500 / 4.31 ( 3381) Misc. bond : bond 0.00442 / 0.30 ( 40) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.888 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: 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: symmetry clash REVERT: A 303 ARG cc_start: 0.8615 (ptp-170) cc_final: 0.8409 (ttp-110) REVERT: A 552 LEU cc_start: 0.9594 (tt) cc_final: 0.9272 (mt) REVERT: B 640 LEU cc_start: 0.8304 (tt) cc_final: 0.7909 (tp) REVERT: C 709 LYS cc_start: 0.9533 (tptt) cc_final: 0.9290 (tppt) REVERT: C 720 MET cc_start: 0.8690 (mmm) cc_final: 0.8412 (mtp) REVERT: C 724 TYR cc_start: 0.9278 (m-10) cc_final: 0.8980 (m-10) REVERT: D 408 HIS cc_start: 0.9477 (t-90) cc_final: 0.9241 (t70) REVERT: D 444 LEU cc_start: 0.9382 (tp) cc_final: 0.9164 (mm) REVERT: D 453 MET cc_start: 0.9069 (mmp) cc_final: 0.8691 (mtt) REVERT: D 603 ASP cc_start: 0.8508 (t0) cc_final: 0.8264 (t70) REVERT: D 629 LEU cc_start: 0.9437 (mt) cc_final: 0.9159 (mt) REVERT: D 712 MET cc_start: 0.9326 (tmm) cc_final: 0.9047 (tmm) REVERT: E 573 MET cc_start: 0.8119 (mmp) cc_final: 0.7693 (mmp) REVERT: E 585 MET cc_start: 0.8761 (tmm) cc_final: 0.8238 (tmm) REVERT: E 589 PHE cc_start: 0.8335 (m-10) cc_final: 0.8017 (m-80) REVERT: E 655 MET cc_start: 0.8884 (mpp) cc_final: 0.8341 (mpp) REVERT: E 657 MET cc_start: 0.9349 (mmp) cc_final: 0.9027 (mmm) REVERT: E 709 LYS cc_start: 0.9440 (tptt) cc_final: 0.9227 (tppt) REVERT: E 712 MET cc_start: 0.9392 (tpp) cc_final: 0.9177 (tpt) REVERT: E 720 MET cc_start: 0.8176 (tpp) cc_final: 0.7910 (tpp) REVERT: F 585 MET cc_start: 0.8709 (tmm) cc_final: 0.8479 (tmm) REVERT: F 724 TYR cc_start: 0.8920 (m-80) cc_final: 0.8627 (m-80) outliers start: 2 outliers final: 0 residues processed: 264 average time/residue: 0.1661 time to fit residues: 66.5909 Evaluate side-chains 180 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 119 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS B 352 ASN B 374 ASN B 526 GLN B 546 HIS C 526 GLN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS F 526 GLN F 530 ASN ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.031631 restraints weight = 199905.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.032291 restraints weight = 145328.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.032803 restraints weight = 114309.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.033196 restraints weight = 93776.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.033531 restraints weight = 79813.126| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21879 Z= 0.240 Angle : 0.827 10.060 29696 Z= 0.432 Chirality : 0.045 0.435 3530 Planarity : 0.006 0.093 3801 Dihedral : 7.347 79.227 3056 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.15 % Favored : 94.19 % Rotamer: Outliers : 0.24 % Allowed : 5.06 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 2857 helix: 0.75 (0.13), residues: 1529 sheet: 1.90 (0.25), residues: 376 loop : -1.03 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 607 TYR 0.019 0.002 TYR F 502 PHE 0.038 0.003 PHE A 231 TRP 0.012 0.002 TRP E 510 HIS 0.011 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (21839) covalent geometry : angle 0.82669 / 0.43 (29696) hydrogen bonds : bond 0.04809 / 3.34 ( 1139) hydrogen bonds : angle 5.74804 / 4.27 ( 3381) Misc. bond : bond 0.00318 / 0.21 ( 40) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 213 time to evaluate : 0.845 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: 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 271 ARG cc_start: 0.8820 (ptp-110) cc_final: 0.8508 (ptp-170) REVERT: A 552 LEU cc_start: 0.9604 (tt) cc_final: 0.9343 (mt) REVERT: A 652 LEU cc_start: 0.9355 (mt) cc_final: 0.9078 (mp) REVERT: B 573 MET cc_start: 0.8591 (ptp) cc_final: 0.8318 (ptp) REVERT: B 640 LEU cc_start: 0.8283 (tt) cc_final: 0.7875 (tp) REVERT: D 408 HIS cc_start: 0.9311 (t-90) cc_final: 0.9055 (t70) REVERT: D 593 TYR cc_start: 0.7647 (m-10) cc_final: 0.7162 (m-80) REVERT: D 603 ASP cc_start: 0.8437 (t0) cc_final: 0.7912 (t0) REVERT: D 712 MET cc_start: 0.9308 (tmm) cc_final: 0.9047 (tmm) REVERT: E 573 MET cc_start: 0.8297 (mmp) cc_final: 0.7748 (mmp) REVERT: E 657 MET cc_start: 0.9211 (mmp) cc_final: 0.8874 (mmm) REVERT: E 712 MET cc_start: 0.9335 (tpp) cc_final: 0.9132 (tpt) REVERT: E 720 MET cc_start: 0.8177 (tpp) cc_final: 0.7708 (tpp) REVERT: F 724 TYR cc_start: 0.8832 (m-80) cc_final: 0.8510 (m-80) outliers start: 5 outliers final: 2 residues processed: 218 average time/residue: 0.1556 time to fit residues: 53.4611 Evaluate side-chains 165 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 40.0000 chunk 20 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 526 GLN B 659 ASN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** 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 = 0.3143 r_free = 0.3143 target = 0.042944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.031487 restraints weight = 200146.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.032130 restraints weight = 144163.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.032667 restraints weight = 112123.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.033037 restraints weight = 91654.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.033353 restraints weight = 78369.264| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21879 Z= 0.207 Angle : 0.757 10.842 29696 Z= 0.395 Chirality : 0.044 0.406 3530 Planarity : 0.006 0.081 3801 Dihedral : 7.116 87.140 3056 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.01 % Favored : 94.47 % Rotamer: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 2857 helix: 0.70 (0.13), residues: 1525 sheet: 1.44 (0.25), residues: 379 loop : -0.92 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 315 TYR 0.014 0.002 TYR F 502 PHE 0.033 0.002 PHE A 231 TRP 0.011 0.002 TRP E 510 HIS 0.010 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (21839) covalent geometry : angle 0.75684 / 0.39 (29696) hydrogen bonds : bond 0.04376 / 3.04 ( 1139) hydrogen bonds : angle 5.59428 / 4.15 ( 3381) Misc. bond : bond 0.00328 / 0.22 ( 40) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.798 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: 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 271 ARG cc_start: 0.8847 (ptp-110) cc_final: 0.8568 (ptp-170) REVERT: A 552 LEU cc_start: 0.9615 (tt) cc_final: 0.9337 (mt) REVERT: B 368 LEU cc_start: 0.9024 (pp) cc_final: 0.8591 (mm) REVERT: B 370 ILE cc_start: 0.8981 (pt) cc_final: 0.8640 (tp) REVERT: B 640 LEU cc_start: 0.8359 (tt) cc_final: 0.8156 (tp) REVERT: C 499 TYR cc_start: 0.8098 (m-10) cc_final: 0.7750 (m-10) REVERT: C 610 ASP cc_start: 0.8795 (t0) cc_final: 0.8585 (t0) REVERT: C 657 MET cc_start: 0.8917 (mmp) cc_final: 0.8693 (mmm) REVERT: D 354 LEU cc_start: 0.9185 (mm) cc_final: 0.8938 (pp) REVERT: D 573 MET cc_start: 0.8879 (ttm) cc_final: 0.8648 (ttm) REVERT: D 593 TYR cc_start: 0.7970 (m-10) cc_final: 0.7693 (m-80) REVERT: D 603 ASP cc_start: 0.8720 (t0) cc_final: 0.8264 (t0) REVERT: D 716 MET cc_start: 0.9262 (mtt) cc_final: 0.8999 (tmm) REVERT: D 720 MET cc_start: 0.8406 (mpp) cc_final: 0.7744 (mpp) REVERT: E 657 MET cc_start: 0.9317 (mmp) cc_final: 0.8975 (mmm) REVERT: E 720 MET cc_start: 0.8468 (tpp) cc_final: 0.7990 (tpp) REVERT: F 504 MET cc_start: 0.9045 (pmm) cc_final: 0.8830 (pmm) REVERT: F 724 TYR cc_start: 0.9006 (m-80) cc_final: 0.8688 (m-80) outliers start: 1 outliers final: 1 residues processed: 202 average time/residue: 0.1501 time to fit residues: 48.2565 Evaluate side-chains 159 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 29 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 526 GLN C 252 HIS ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 GLN D 530 ASN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 ASN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.042597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.031171 restraints weight = 196631.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.031831 restraints weight = 144757.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032345 restraints weight = 113553.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.032756 restraints weight = 93305.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033081 restraints weight = 79466.868| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21879 Z= 0.187 Angle : 0.734 9.777 29696 Z= 0.378 Chirality : 0.043 0.381 3530 Planarity : 0.005 0.077 3801 Dihedral : 6.997 88.171 3056 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.32 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 2857 helix: 0.75 (0.13), residues: 1528 sheet: 1.16 (0.24), residues: 390 loop : -0.89 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 315 TYR 0.013 0.002 TYR F 611 PHE 0.027 0.002 PHE A 231 TRP 0.009 0.001 TRP E 510 HIS 0.009 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (21839) covalent geometry : angle 0.73357 / 0.38 (29696) hydrogen bonds : bond 0.04194 / 2.90 ( 1139) hydrogen bonds : angle 5.50816 / 4.09 ( 3381) Misc. bond : bond 0.00360 / 0.24 ( 40) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.894 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: symmetry clash REVERT: A 271 ARG cc_start: 0.8854 (ptp-110) cc_final: 0.8552 (ptp-170) REVERT: A 552 LEU cc_start: 0.9601 (tt) cc_final: 0.9315 (mt) REVERT: A 578 GLU cc_start: 0.8312 (tt0) cc_final: 0.7478 (tm-30) REVERT: B 368 LEU cc_start: 0.8995 (pp) cc_final: 0.8591 (mm) REVERT: B 370 ILE cc_start: 0.8998 (pt) cc_final: 0.8688 (tp) REVERT: B 587 LYS cc_start: 0.9396 (pptt) cc_final: 0.9090 (pptt) REVERT: C 499 TYR cc_start: 0.8131 (m-10) cc_final: 0.7804 (m-10) REVERT: C 599 CYS cc_start: 0.9275 (t) cc_final: 0.9011 (t) REVERT: C 610 ASP cc_start: 0.8894 (t0) cc_final: 0.8625 (t0) REVERT: D 354 LEU cc_start: 0.9198 (mm) cc_final: 0.8953 (pp) REVERT: D 593 TYR cc_start: 0.8008 (m-10) cc_final: 0.7703 (m-80) REVERT: D 603 ASP cc_start: 0.8706 (t0) cc_final: 0.8268 (t0) REVERT: D 657 MET cc_start: 0.9049 (ttp) cc_final: 0.8616 (ptt) REVERT: D 709 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9336 (mttt) REVERT: E 585 MET cc_start: 0.9390 (tpt) cc_final: 0.9172 (tpp) REVERT: E 657 MET cc_start: 0.9332 (mmp) cc_final: 0.9061 (mmm) REVERT: E 712 MET cc_start: 0.9425 (tpt) cc_final: 0.8983 (mtp) REVERT: E 720 MET cc_start: 0.8390 (tpp) cc_final: 0.7842 (tpp) REVERT: F 720 MET cc_start: 0.9220 (mmp) cc_final: 0.8897 (mmt) REVERT: F 724 TYR cc_start: 0.8989 (m-80) cc_final: 0.8705 (m-80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1430 time to fit residues: 44.1761 Evaluate side-chains 161 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 15 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 186 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN C 417 HIS C 583 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN E 374 ASN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.030314 restraints weight = 204315.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.030933 restraints weight = 146668.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.031430 restraints weight = 114763.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.031789 restraints weight = 93806.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.032099 restraints weight = 79945.236| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21879 Z= 0.257 Angle : 0.799 10.966 29696 Z= 0.416 Chirality : 0.045 0.369 3530 Planarity : 0.006 0.079 3801 Dihedral : 7.214 82.028 3056 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.74 % Favored : 93.66 % Rotamer: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 2857 helix: 0.45 (0.13), residues: 1543 sheet: 0.70 (0.24), residues: 388 loop : -1.05 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 315 TYR 0.019 0.002 TYR D 611 PHE 0.027 0.002 PHE A 231 TRP 0.013 0.002 TRP A 704 HIS 0.010 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 (21839) covalent geometry : angle 0.79903 / 0.42 (29696) hydrogen bonds : bond 0.04445 / 3.10 ( 1139) hydrogen bonds : angle 5.79472 / 4.31 ( 3381) Misc. bond : bond 0.00284 / 0.19 ( 40) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.862 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.9593 (tt) cc_final: 0.9326 (mt) REVERT: A 578 GLU cc_start: 0.8298 (tt0) cc_final: 0.7511 (tm-30) REVERT: B 368 LEU cc_start: 0.8981 (pp) cc_final: 0.8591 (mm) REVERT: B 370 ILE cc_start: 0.9032 (pt) cc_final: 0.8749 (tp) REVERT: B 573 MET cc_start: 0.8866 (ptp) cc_final: 0.8499 (ptp) REVERT: B 587 LYS cc_start: 0.9393 (pptt) cc_final: 0.9163 (pptt) REVERT: C 499 TYR cc_start: 0.8181 (m-10) cc_final: 0.7946 (m-10) REVERT: C 583 GLN cc_start: 0.9087 (mt0) cc_final: 0.8867 (mt0) REVERT: C 657 MET cc_start: 0.8975 (mmp) cc_final: 0.8667 (mmm) REVERT: D 453 MET cc_start: 0.9151 (mmp) cc_final: 0.8823 (mtt) REVERT: D 573 MET cc_start: 0.8851 (ttm) cc_final: 0.8547 (ttm) REVERT: D 585 MET cc_start: 0.9306 (mmp) cc_final: 0.9047 (mmp) REVERT: D 593 TYR cc_start: 0.8134 (m-10) cc_final: 0.7734 (m-80) REVERT: D 603 ASP cc_start: 0.8605 (t0) cc_final: 0.8259 (t0) REVERT: E 585 MET cc_start: 0.9314 (tpt) cc_final: 0.8886 (tpt) REVERT: E 589 PHE cc_start: 0.8728 (m-10) cc_final: 0.7868 (m-80) REVERT: E 657 MET cc_start: 0.9305 (mmp) cc_final: 0.9005 (mmm) REVERT: E 712 MET cc_start: 0.9430 (tpt) cc_final: 0.9000 (mtt) REVERT: E 720 MET cc_start: 0.8466 (tpp) cc_final: 0.7939 (tpp) REVERT: F 504 MET cc_start: 0.9042 (pmm) cc_final: 0.8800 (pmm) REVERT: F 724 TYR cc_start: 0.8970 (m-80) cc_final: 0.8735 (m-80) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1370 time to fit residues: 41.4238 Evaluate side-chains 154 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 150 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 0.0060 chunk 178 optimal weight: 1.9990 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 526 GLN B 659 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 GLN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.042730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.031203 restraints weight = 193059.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.031882 restraints weight = 140484.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.032422 restraints weight = 109633.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032824 restraints weight = 89465.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033156 restraints weight = 76230.633| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 21879 Z= 0.148 Angle : 0.725 13.514 29696 Z= 0.368 Chirality : 0.043 0.320 3530 Planarity : 0.005 0.073 3801 Dihedral : 7.077 87.948 3056 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.97 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2857 helix: 0.78 (0.13), residues: 1538 sheet: 0.74 (0.25), residues: 390 loop : -0.92 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 315 TYR 0.015 0.001 TYR F 259 PHE 0.024 0.002 PHE A 231 TRP 0.008 0.001 TRP F 510 HIS 0.008 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (21839) covalent geometry : angle 0.72524 / 0.37 (29696) hydrogen bonds : bond 0.03900 / 2.70 ( 1139) hydrogen bonds : angle 5.39210 / 4.01 ( 3381) Misc. bond : bond 0.00405 / 0.28 ( 40) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.836 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.8841 (ptp-110) cc_final: 0.8547 (ptp-170) REVERT: A 552 LEU cc_start: 0.9566 (tt) cc_final: 0.9258 (mt) REVERT: A 573 MET cc_start: 0.9145 (mmp) cc_final: 0.8873 (mmm) REVERT: A 578 GLU cc_start: 0.8404 (tt0) cc_final: 0.7652 (tm-30) REVERT: B 306 PHE cc_start: 0.8505 (m-80) cc_final: 0.8252 (m-80) REVERT: B 368 LEU cc_start: 0.8878 (pp) cc_final: 0.8502 (mm) REVERT: B 370 ILE cc_start: 0.8964 (pt) cc_final: 0.8606 (tp) REVERT: B 587 LYS cc_start: 0.9381 (pptt) cc_final: 0.9114 (pptt) REVERT: C 304 LYS cc_start: 0.9332 (pptt) cc_final: 0.9026 (pttp) REVERT: C 657 MET cc_start: 0.9007 (mmp) cc_final: 0.8743 (mmm) REVERT: D 590 ASP cc_start: 0.8881 (m-30) cc_final: 0.8499 (m-30) REVERT: D 593 TYR cc_start: 0.8148 (m-10) cc_final: 0.7942 (m-80) REVERT: D 603 ASP cc_start: 0.8617 (t0) cc_final: 0.8291 (t0) REVERT: D 657 MET cc_start: 0.9147 (ttp) cc_final: 0.8704 (ptt) REVERT: D 709 LYS cc_start: 0.9533 (mmmt) cc_final: 0.9306 (mttt) REVERT: E 585 MET cc_start: 0.9238 (tpt) cc_final: 0.8841 (tpt) REVERT: E 655 MET cc_start: 0.8805 (mpp) cc_final: 0.8375 (mmm) REVERT: E 657 MET cc_start: 0.9318 (mmp) cc_final: 0.9089 (mmm) REVERT: E 712 MET cc_start: 0.9439 (tpt) cc_final: 0.8913 (mtp) REVERT: E 720 MET cc_start: 0.8404 (tpp) cc_final: 0.7877 (tpp) REVERT: F 720 MET cc_start: 0.9132 (mmp) cc_final: 0.8887 (mmp) REVERT: F 724 TYR cc_start: 0.9011 (m-80) cc_final: 0.8768 (m-80) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1470 time to fit residues: 46.4183 Evaluate side-chains 163 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 243 optimal weight: 10.0000 chunk 277 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 22 optimal weight: 30.0000 chunk 188 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN B 454 ASN B 526 GLN B 659 ASN C 583 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.042121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.030820 restraints weight = 198274.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.031487 restraints weight = 143794.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032006 restraints weight = 111931.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032394 restraints weight = 91356.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.032725 restraints weight = 77538.221| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21879 Z= 0.167 Angle : 0.716 10.894 29696 Z= 0.368 Chirality : 0.043 0.298 3530 Planarity : 0.005 0.068 3801 Dihedral : 6.975 85.480 3056 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.39 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2857 helix: 0.76 (0.13), residues: 1535 sheet: 0.64 (0.25), residues: 391 loop : -0.96 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 315 TYR 0.017 0.002 TYR F 259 PHE 0.024 0.002 PHE A 231 TRP 0.008 0.001 TRP E 510 HIS 0.009 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (21839) covalent geometry : angle 0.71593 / 0.37 (29696) hydrogen bonds : bond 0.03931 / 2.73 ( 1139) hydrogen bonds : angle 5.44600 / 4.06 ( 3381) Misc. bond : bond 0.00361 / 0.25 ( 40) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.795 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.8853 (ptp-110) cc_final: 0.8577 (ptp-170) REVERT: A 552 LEU cc_start: 0.9541 (tt) cc_final: 0.9249 (mt) REVERT: A 573 MET cc_start: 0.9151 (mmp) cc_final: 0.8912 (mmm) REVERT: B 368 LEU cc_start: 0.8869 (pp) cc_final: 0.8498 (mm) REVERT: B 370 ILE cc_start: 0.8957 (pt) cc_final: 0.8603 (tp) REVERT: B 573 MET cc_start: 0.8926 (ptp) cc_final: 0.8564 (ptp) REVERT: B 587 LYS cc_start: 0.9370 (pptt) cc_final: 0.9129 (pptt) REVERT: C 304 LYS cc_start: 0.9341 (pptt) cc_final: 0.9086 (pttp) REVERT: C 568 CYS cc_start: 0.7917 (t) cc_final: 0.7325 (t) REVERT: C 599 CYS cc_start: 0.9286 (t) cc_final: 0.9086 (t) REVERT: C 657 MET cc_start: 0.8987 (mmp) cc_final: 0.8717 (mmm) REVERT: D 593 TYR cc_start: 0.8182 (m-10) cc_final: 0.7800 (m-80) REVERT: D 603 ASP cc_start: 0.8587 (t0) cc_final: 0.8246 (t0) REVERT: E 585 MET cc_start: 0.9273 (tpt) cc_final: 0.8877 (tpt) REVERT: E 712 MET cc_start: 0.9449 (tpt) cc_final: 0.8915 (mtp) REVERT: E 720 MET cc_start: 0.8419 (tpp) cc_final: 0.7877 (tpp) REVERT: F 720 MET cc_start: 0.9149 (mmp) cc_final: 0.8890 (mmt) REVERT: F 724 TYR cc_start: 0.8993 (m-80) cc_final: 0.8774 (m-80) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1397 time to fit residues: 40.6430 Evaluate side-chains 155 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 146 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN B 659 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.041577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.030347 restraints weight = 199898.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.031013 restraints weight = 145184.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.031501 restraints weight = 112953.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.031904 restraints weight = 92378.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.032205 restraints weight = 78466.155| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 21879 Z= 0.201 Angle : 0.743 17.420 29696 Z= 0.383 Chirality : 0.043 0.280 3530 Planarity : 0.005 0.072 3801 Dihedral : 6.993 83.194 3056 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.67 % Favored : 93.77 % Rotamer: Outliers : 0.05 % Allowed : 1.10 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2857 helix: 0.62 (0.13), residues: 1550 sheet: 0.47 (0.25), residues: 388 loop : -1.06 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 315 TYR 0.015 0.002 TYR A 499 PHE 0.023 0.002 PHE A 231 TRP 0.009 0.002 TRP E 510 HIS 0.010 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (21839) covalent geometry : angle 0.74284 / 0.38 (29696) hydrogen bonds : bond 0.04065 / 2.82 ( 1139) hydrogen bonds : angle 5.58347 / 4.15 ( 3381) Misc. bond : bond 0.00335 / 0.23 ( 40) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.869 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: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.8863 (ptp-110) cc_final: 0.8611 (ptp-170) REVERT: A 552 LEU cc_start: 0.9539 (tt) cc_final: 0.9258 (mt) REVERT: A 578 GLU cc_start: 0.8242 (pp20) cc_final: 0.7950 (tm-30) REVERT: B 368 LEU cc_start: 0.8956 (pp) cc_final: 0.8614 (mm) REVERT: B 720 MET cc_start: 0.9007 (mmp) cc_final: 0.8806 (mmm) REVERT: C 568 CYS cc_start: 0.7721 (t) cc_final: 0.6758 (t) REVERT: C 655 MET cc_start: 0.9099 (mmp) cc_final: 0.8868 (mmm) REVERT: C 657 MET cc_start: 0.8994 (mmp) cc_final: 0.8708 (mmm) REVERT: D 585 MET cc_start: 0.9327 (mmp) cc_final: 0.9061 (mmp) REVERT: D 593 TYR cc_start: 0.8246 (m-10) cc_final: 0.7826 (m-80) REVERT: D 603 ASP cc_start: 0.8677 (t0) cc_final: 0.8362 (t0) REVERT: D 655 MET cc_start: 0.8336 (ptp) cc_final: 0.7929 (ptt) REVERT: D 657 MET cc_start: 0.9206 (ttp) cc_final: 0.8771 (ptm) REVERT: E 585 MET cc_start: 0.9288 (tpt) cc_final: 0.8970 (tpp) REVERT: E 712 MET cc_start: 0.9446 (tpt) cc_final: 0.8926 (mtp) REVERT: E 720 MET cc_start: 0.8404 (tpp) cc_final: 0.7854 (tpp) REVERT: F 504 MET cc_start: 0.8976 (pmm) cc_final: 0.8747 (pmm) REVERT: F 720 MET cc_start: 0.9163 (mmp) cc_final: 0.8897 (mmt) REVERT: F 724 TYR cc_start: 0.9010 (m-80) cc_final: 0.8750 (m-80) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1297 time to fit residues: 37.6862 Evaluate side-chains 154 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 69 optimal weight: 0.6980 chunk 228 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 271 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 101 optimal weight: 0.0070 chunk 128 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 ASN B 505 ASN B 526 GLN B 659 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN D 408 HIS ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.042277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.030877 restraints weight = 196964.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.031572 restraints weight = 142831.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.032104 restraints weight = 110689.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.032521 restraints weight = 89849.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.032839 restraints weight = 75633.045| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 21879 Z= 0.150 Angle : 0.717 14.462 29696 Z= 0.366 Chirality : 0.043 0.283 3530 Planarity : 0.005 0.071 3801 Dihedral : 6.862 83.029 3056 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.11 % Favored : 94.36 % Rotamer: Outliers : 0.05 % Allowed : 0.72 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2857 helix: 0.75 (0.13), residues: 1544 sheet: 0.41 (0.25), residues: 387 loop : -1.02 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 315 TYR 0.017 0.001 TYR C 499 PHE 0.022 0.001 PHE A 231 TRP 0.006 0.001 TRP A 510 HIS 0.010 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (21839) covalent geometry : angle 0.71663 / 0.37 (29696) hydrogen bonds : bond 0.03881 / 2.69 ( 1139) hydrogen bonds : angle 5.40068 / 4.02 ( 3381) Misc. bond : bond 0.00412 / 0.28 ( 40) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.843 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: symmetry clash revert: symmetry clash REVERT: A 271 ARG cc_start: 0.8838 (ptp-110) cc_final: 0.8568 (ptp-170) REVERT: A 552 LEU cc_start: 0.9522 (tt) cc_final: 0.9259 (mt) REVERT: A 573 MET cc_start: 0.9171 (mmp) cc_final: 0.8836 (mmm) REVERT: B 370 ILE cc_start: 0.8924 (pt) cc_final: 0.8591 (tp) REVERT: B 573 MET cc_start: 0.8909 (ptp) cc_final: 0.8551 (ptp) REVERT: B 587 LYS cc_start: 0.9400 (pptt) cc_final: 0.9125 (pptt) REVERT: C 304 LYS cc_start: 0.9344 (pptt) cc_final: 0.9073 (pttp) REVERT: C 499 TYR cc_start: 0.8278 (m-10) cc_final: 0.8016 (m-10) REVERT: C 657 MET cc_start: 0.9044 (mmp) cc_final: 0.8785 (mmm) REVERT: D 585 MET cc_start: 0.9345 (mmp) cc_final: 0.9096 (mmp) REVERT: D 593 TYR cc_start: 0.8219 (m-10) cc_final: 0.7818 (m-80) REVERT: D 603 ASP cc_start: 0.8630 (t0) cc_final: 0.8300 (t0) REVERT: D 655 MET cc_start: 0.8315 (ptp) cc_final: 0.8107 (ptt) REVERT: D 657 MET cc_start: 0.9143 (ttp) cc_final: 0.8659 (ptm) REVERT: E 585 MET cc_start: 0.9241 (tpt) cc_final: 0.8785 (tpt) REVERT: E 589 PHE cc_start: 0.8740 (m-10) cc_final: 0.7965 (m-80) REVERT: E 657 MET cc_start: 0.9202 (mmp) cc_final: 0.8978 (mmm) REVERT: E 712 MET cc_start: 0.9459 (tpt) cc_final: 0.8904 (mtp) REVERT: E 720 MET cc_start: 0.8371 (tpp) cc_final: 0.7816 (tpp) REVERT: F 372 MET cc_start: 0.4789 (ppp) cc_final: 0.4460 (tpp) REVERT: F 657 MET cc_start: 0.8802 (mmp) cc_final: 0.8356 (tpt) REVERT: F 661 PHE cc_start: 0.8635 (m-80) cc_final: 0.8370 (m-80) REVERT: F 716 MET cc_start: 0.8998 (ptp) cc_final: 0.8735 (tpt) REVERT: F 720 MET cc_start: 0.9153 (mmp) cc_final: 0.8579 (mmm) REVERT: F 724 TYR cc_start: 0.8978 (m-80) cc_final: 0.8752 (m-80) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1322 time to fit residues: 39.4746 Evaluate side-chains 153 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 211 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 68 optimal weight: 0.1980 chunk 262 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 ASN B 526 GLN B 659 ASN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** E 505 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 = 0.3134 r_free = 0.3134 target = 0.042507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.031097 restraints weight = 197766.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.031781 restraints weight = 143297.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032269 restraints weight = 111844.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.032696 restraints weight = 91704.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.033044 restraints weight = 77202.593| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.6613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 21879 Z= 0.144 Angle : 0.706 13.191 29696 Z= 0.357 Chirality : 0.042 0.285 3530 Planarity : 0.005 0.070 3801 Dihedral : 6.765 82.666 3056 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.83 % Favored : 94.61 % Rotamer: Outliers : 0.05 % Allowed : 0.72 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.16), residues: 2857 helix: 0.84 (0.13), residues: 1542 sheet: 0.34 (0.25), residues: 394 loop : -1.03 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 315 TYR 0.012 0.001 TYR F 259 PHE 0.021 0.001 PHE A 231 TRP 0.006 0.001 TRP F 510 HIS 0.009 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21839) covalent geometry : angle 0.70644 / 0.36 (29696) hydrogen bonds : bond 0.03763 / 2.60 ( 1139) hydrogen bonds : angle 5.32336 / 3.96 ( 3381) Misc. bond : bond 0.00385 / 0.26 ( 40) =============================================================================== Job complete usr+sys time: 3911.23 seconds wall clock time: 68 minutes 48.17 seconds (4128.17 seconds total)