Starting phenix.real_space_refine on Thu Sep 18 23:53:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j94_6204/09_2025/3j94_6204.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j94_6204/09_2025/3j94_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_2025/3j94_6204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2025/3j94_6204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2025/3j94_6204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j94_6204/09_2025/3j94_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-2.0-5805/lib/python3.9/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: 5.41, per 1000 atoms: 0.25 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: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.88 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: 4.18 Time building geometry restraints manager: 3.09 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 - 17.99: 11930 17.99 - 35.97: 1082 35.97 - 53.96: 344 53.96 - 71.95: 115 71.95 - 89.93: 47 Dihedral angle restraints: 13518 sinusoidal: 5242 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 13515 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.200 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 17.137 89.934 8158 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 aren 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 covalent geometry : bond 0.00941 (21839) covalent geometry : angle 1.96512 (29696) hydrogen bonds : bond 0.18805 ( 1139) hydrogen bonds : angle 7.65339 ( 3381) Misc. bond : bond 0.20974 ( 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 : 0.776 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: 0.8519 (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: 0.9287 (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: 0.9022 (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: 0.1788 time to fit residues: 126.7771 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 : 0.955 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.044890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033042 restraints weight = 183669.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033723 restraints weight = 136859.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034253 restraints weight = 108951.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034680 restraints weight = 90283.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.034999 restraints weight = 77701.430| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21879 Z= 0.218 Angle : 0.899 13.003 29696 Z= 0.465 Chirality : 0.047 0.433 3530 Planarity : 0.006 0.078 3801 Dihedral : 12.661 87.606 3397 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.81 % Allowed : 3.78 % Favored : 95.41 % Rotamer: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % 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 aren not related in a simple way. whole: 1.13 (0.15), residues: 2857 helix: 1.34 (0.12), residues: 1527 sheet: 2.71 (0.25), residues: 363 loop : -0.99 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 691 TYR 0.018 0.002 TYR C 499 PHE 0.047 0.003 PHE A 231 TRP 0.019 0.002 TRP A 510 HIS 0.011 0.002 HIS D 546 Details of bonding type rmsd covalent geometry : bond 0.00473 (21839) covalent geometry : angle 0.89884 (29696) hydrogen bonds : bond 0.05496 ( 1139) hydrogen bonds : angle 5.78480 ( 3381) Misc. bond : bond 0.00410 ( 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 263 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.851 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: A 552 LEU cc_start: 0.9598 (tt) cc_final: 0.9329 (mt) REVERT: A 652 LEU cc_start: 0.9394 (mp) cc_final: 0.9089 (pp) REVERT: B 640 LEU cc_start: 0.8294 (tt) cc_final: 0.7900 (tp) REVERT: C 709 LYS cc_start: 0.9530 (tptt) cc_final: 0.9292 (tppt) REVERT: C 720 MET cc_start: 0.8681 (mmm) cc_final: 0.8402 (mtp) REVERT: C 724 TYR cc_start: 0.9273 (m-10) cc_final: 0.8976 (m-10) REVERT: D 381 GLU cc_start: 0.8685 (mp0) cc_final: 0.8481 (pm20) REVERT: D 408 HIS cc_start: 0.9467 (t-90) cc_final: 0.9226 (t70) REVERT: D 444 LEU cc_start: 0.9377 (tp) cc_final: 0.9162 (mm) REVERT: D 453 MET cc_start: 0.9102 (mmp) cc_final: 0.8708 (mtt) REVERT: D 603 ASP cc_start: 0.8501 (t0) cc_final: 0.8257 (t70) REVERT: D 629 LEU cc_start: 0.9439 (mt) cc_final: 0.9158 (mt) REVERT: D 712 MET cc_start: 0.9313 (tmm) cc_final: 0.9041 (tmm) REVERT: E 573 MET cc_start: 0.8117 (mmp) cc_final: 0.7684 (mmp) REVERT: E 585 MET cc_start: 0.8758 (tmm) cc_final: 0.8229 (tmm) REVERT: E 589 PHE cc_start: 0.8359 (m-10) cc_final: 0.8046 (m-80) REVERT: E 655 MET cc_start: 0.8812 (mpp) cc_final: 0.8268 (mpp) REVERT: E 657 MET cc_start: 0.9345 (mmp) cc_final: 0.9020 (mmm) REVERT: E 709 LYS cc_start: 0.9434 (tptt) cc_final: 0.9201 (tppt) REVERT: E 712 MET cc_start: 0.9390 (tpp) cc_final: 0.9172 (tpt) REVERT: E 720 MET cc_start: 0.8180 (tpp) cc_final: 0.7910 (tpp) REVERT: F 724 TYR cc_start: 0.8914 (m-80) cc_final: 0.8623 (m-80) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.1802 time to fit residues: 70.8773 Evaluate side-chains 182 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 4.9990 chunk 271 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS B 352 ASN B 526 GLN B 546 HIS C 505 ASN 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.032061 restraints weight = 195298.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.032753 restraints weight = 143985.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033286 restraints weight = 112893.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033695 restraints weight = 92782.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.034027 restraints weight = 79019.214| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21879 Z= 0.211 Angle : 0.801 10.012 29696 Z= 0.416 Chirality : 0.044 0.430 3530 Planarity : 0.006 0.090 3801 Dihedral : 11.820 83.711 3397 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.94 % Favored : 94.43 % Rotamer: Outliers : 0.29 % Allowed : 5.01 % 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 aren not related in a simple way. whole: 0.61 (0.15), residues: 2857 helix: 0.88 (0.13), residues: 1528 sheet: 2.03 (0.26), residues: 375 loop : -1.00 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 607 TYR 0.017 0.002 TYR F 502 PHE 0.038 0.002 PHE A 231 TRP 0.012 0.002 TRP F 510 HIS 0.011 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00456 (21839) covalent geometry : angle 0.80088 (29696) hydrogen bonds : bond 0.04684 ( 1139) hydrogen bonds : angle 5.61733 ( 3381) Misc. bond : bond 0.00325 ( 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 227 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 221 time to evaluate : 0.878 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: 0.8812 (ptp-110) cc_final: 0.8504 (ptp-170) REVERT: A 552 LEU cc_start: 0.9606 (tt) cc_final: 0.9341 (mt) REVERT: A 573 MET cc_start: 0.8971 (mmm) cc_final: 0.8734 (mmm) REVERT: A 655 MET cc_start: 0.8396 (mtm) cc_final: 0.8166 (mtp) REVERT: B 640 LEU cc_start: 0.8264 (tt) cc_final: 0.7839 (tp) REVERT: C 709 LYS cc_start: 0.9555 (tptt) cc_final: 0.9316 (tppt) REVERT: C 720 MET cc_start: 0.8653 (mmm) cc_final: 0.8365 (mtp) REVERT: D 453 MET cc_start: 0.9101 (mmp) cc_final: 0.8761 (mtt) REVERT: D 581 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8901 (mmtt) REVERT: D 593 TYR cc_start: 0.7627 (m-10) cc_final: 0.7180 (m-80) REVERT: D 603 ASP cc_start: 0.8463 (t0) cc_final: 0.7999 (t0) REVERT: D 709 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9163 (mtmm) REVERT: D 712 MET cc_start: 0.9271 (tmm) cc_final: 0.9035 (tmm) REVERT: E 657 MET cc_start: 0.9222 (mmp) cc_final: 0.8908 (mmm) REVERT: E 712 MET cc_start: 0.9349 (tpp) cc_final: 0.9134 (tpt) REVERT: E 720 MET cc_start: 0.8205 (tpp) cc_final: 0.7773 (tpp) REVERT: F 724 TYR cc_start: 0.8855 (m-80) cc_final: 0.8508 (m-80) outliers start: 6 outliers final: 3 residues processed: 227 average time/residue: 0.1653 time to fit residues: 58.5935 Evaluate side-chains 169 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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: 30.0000 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 156 optimal weight: 0.0010 chunk 283 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 overall best weight: 2.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 624 GLN ** 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 417 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.032133 restraints weight = 193945.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.032812 restraints weight = 141754.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.033366 restraints weight = 110957.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.033758 restraints weight = 90846.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.034103 restraints weight = 77497.208| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21879 Z= 0.167 Angle : 0.730 10.920 29696 Z= 0.378 Chirality : 0.043 0.382 3530 Planarity : 0.005 0.075 3801 Dihedral : 11.549 86.277 3397 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.90 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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 aren not related in a simple way. whole: 0.58 (0.15), residues: 2857 helix: 0.89 (0.13), residues: 1531 sheet: 1.67 (0.25), residues: 375 loop : -0.91 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 315 TYR 0.013 0.001 TYR E 502 PHE 0.032 0.002 PHE A 231 TRP 0.010 0.002 TRP F 510 HIS 0.010 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00359 (21839) covalent geometry : angle 0.72968 (29696) hydrogen bonds : bond 0.04176 ( 1139) hydrogen bonds : angle 5.38770 ( 3381) Misc. bond : bond 0.00277 ( 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 208 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.681 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: 0.8777 (ptp-110) cc_final: 0.8535 (ptp-170) REVERT: A 384 LEU cc_start: 0.9055 (mt) cc_final: 0.8847 (mt) REVERT: A 552 LEU cc_start: 0.9613 (tt) cc_final: 0.9339 (mt) REVERT: B 640 LEU cc_start: 0.8261 (tt) cc_final: 0.8043 (tp) REVERT: C 552 LEU cc_start: 0.9477 (mt) cc_final: 0.9273 (mt) REVERT: D 354 LEU cc_start: 0.9152 (mm) cc_final: 0.8922 (pp) REVERT: D 453 MET cc_start: 0.9118 (mmp) cc_final: 0.8748 (mtt) REVERT: D 593 TYR cc_start: 0.7851 (m-10) cc_final: 0.7534 (m-80) REVERT: D 603 ASP cc_start: 0.8481 (t0) cc_final: 0.8011 (t0) REVERT: D 605 ILE cc_start: 0.9451 (mt) cc_final: 0.9229 (mt) REVERT: D 709 LYS cc_start: 0.9552 (mmmt) cc_final: 0.9137 (mtmm) REVERT: D 716 MET cc_start: 0.9167 (mtt) cc_final: 0.8966 (tmm) REVERT: D 720 MET cc_start: 0.8341 (mpp) cc_final: 0.7862 (mpp) REVERT: E 657 MET cc_start: 0.9259 (mmp) cc_final: 0.8936 (mmm) REVERT: E 720 MET cc_start: 0.8421 (tpp) cc_final: 0.7937 (tpp) REVERT: F 724 TYR cc_start: 0.8939 (m-80) cc_final: 0.8679 (m-80) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1588 time to fit residues: 51.6638 Evaluate side-chains 162 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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: 9.9990 chunk 57 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN B 526 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032116 restraints weight = 194180.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.032782 restraints weight = 141253.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033323 restraints weight = 111017.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.033716 restraints weight = 90887.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.034050 restraints weight = 77520.584| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21879 Z= 0.165 Angle : 0.717 9.690 29696 Z= 0.369 Chirality : 0.042 0.374 3530 Planarity : 0.005 0.073 3801 Dihedral : 11.526 87.722 3397 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.01 % Favored : 94.43 % Rotamer: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % 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 aren not related in a simple way. whole: 0.57 (0.15), residues: 2857 helix: 0.91 (0.13), residues: 1523 sheet: 1.46 (0.25), residues: 376 loop : -0.86 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 315 TYR 0.012 0.001 TYR E 502 PHE 0.028 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 covalent geometry : bond 0.00358 (21839) covalent geometry : angle 0.71734 (29696) hydrogen bonds : bond 0.04049 ( 1139) hydrogen bonds : angle 5.33444 ( 3381) Misc. bond : bond 0.00388 ( 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 200 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.909 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: 0.8766 (ptp-110) cc_final: 0.8528 (ptp-170) REVERT: A 384 LEU cc_start: 0.9032 (mt) cc_final: 0.8823 (mt) REVERT: A 552 LEU cc_start: 0.9594 (tt) cc_final: 0.9331 (mt) REVERT: B 368 LEU cc_start: 0.8912 (pp) cc_final: 0.8487 (mm) REVERT: B 370 ILE cc_start: 0.8919 (pt) cc_final: 0.8611 (tp) REVERT: B 587 LYS cc_start: 0.9204 (ptmm) cc_final: 0.8899 (pptt) REVERT: C 585 MET cc_start: 0.9050 (mmp) cc_final: 0.8844 (mmp) REVERT: C 639 LYS cc_start: 0.9245 (mttp) cc_final: 0.8825 (mmtt) REVERT: C 657 MET cc_start: 0.8848 (mmp) cc_final: 0.8643 (mmm) REVERT: D 354 LEU cc_start: 0.9145 (mm) cc_final: 0.8921 (pp) REVERT: D 593 TYR cc_start: 0.7833 (m-10) cc_final: 0.7505 (m-80) REVERT: D 603 ASP cc_start: 0.8531 (t0) cc_final: 0.8134 (t0) REVERT: D 657 MET cc_start: 0.9018 (ttp) cc_final: 0.8727 (ptt) REVERT: D 709 LYS cc_start: 0.9525 (mmmt) cc_final: 0.9154 (mmmt) REVERT: E 589 PHE cc_start: 0.8301 (m-10) cc_final: 0.7989 (m-10) REVERT: E 657 MET cc_start: 0.9203 (mmp) cc_final: 0.8914 (mmm) REVERT: E 720 MET cc_start: 0.8389 (tpp) cc_final: 0.7865 (tpp) REVERT: F 504 MET cc_start: 0.9013 (pmm) cc_final: 0.8769 (pmm) REVERT: F 724 TYR cc_start: 0.8905 (m-80) cc_final: 0.8637 (m-80) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1547 time to fit residues: 49.1599 Evaluate side-chains 159 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 97 optimal weight: 0.0570 chunk 242 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 526 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032082 restraints weight = 192885.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.032752 restraints weight = 140706.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033286 restraints weight = 110554.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033680 restraints weight = 90875.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.034030 restraints weight = 77574.228| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 21879 Z= 0.153 Angle : 0.704 12.550 29696 Z= 0.363 Chirality : 0.042 0.359 3530 Planarity : 0.005 0.070 3801 Dihedral : 11.297 89.301 3397 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.76 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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 aren not related in a simple way. whole: 0.60 (0.16), residues: 2857 helix: 0.95 (0.13), residues: 1529 sheet: 1.29 (0.25), residues: 381 loop : -0.79 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 315 TYR 0.011 0.001 TYR E 502 PHE 0.026 0.002 PHE A 231 TRP 0.015 0.001 TRP F 704 HIS 0.007 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00332 (21839) covalent geometry : angle 0.70399 (29696) hydrogen bonds : bond 0.03955 ( 1139) hydrogen bonds : angle 5.27705 ( 3381) Misc. bond : bond 0.00377 ( 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 202 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.897 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: 0.8769 (ptp-110) cc_final: 0.8526 (ptp-170) REVERT: A 552 LEU cc_start: 0.9567 (tt) cc_final: 0.9306 (mt) REVERT: B 368 LEU cc_start: 0.8899 (pp) cc_final: 0.8503 (mm) REVERT: B 370 ILE cc_start: 0.8931 (pt) cc_final: 0.8668 (tp) REVERT: B 587 LYS cc_start: 0.9208 (ptmm) cc_final: 0.8909 (pptt) REVERT: C 552 LEU cc_start: 0.9484 (mt) cc_final: 0.9281 (mt) REVERT: C 639 LYS cc_start: 0.9184 (mttp) cc_final: 0.8759 (mmtt) REVERT: D 354 LEU cc_start: 0.9149 (mm) cc_final: 0.8898 (pp) REVERT: D 603 ASP cc_start: 0.8513 (t0) cc_final: 0.8104 (t0) REVERT: D 655 MET cc_start: 0.8385 (ptp) cc_final: 0.7838 (ptt) REVERT: D 657 MET cc_start: 0.8977 (ttp) cc_final: 0.8749 (ptm) REVERT: D 709 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9261 (mmmt) REVERT: D 716 MET cc_start: 0.9085 (mtm) cc_final: 0.8853 (mtp) REVERT: E 652 LEU cc_start: 0.9337 (mm) cc_final: 0.9126 (mp) REVERT: E 655 MET cc_start: 0.8747 (mpp) cc_final: 0.8385 (mmm) REVERT: E 657 MET cc_start: 0.9253 (mmp) cc_final: 0.8942 (mmm) REVERT: E 712 MET cc_start: 0.9375 (tpt) cc_final: 0.8954 (mtp) REVERT: E 720 MET cc_start: 0.8341 (tpp) cc_final: 0.7856 (tpp) REVERT: F 720 MET cc_start: 0.9188 (mmp) cc_final: 0.8869 (mmt) REVERT: F 724 TYR cc_start: 0.8882 (m-80) cc_final: 0.8623 (m-80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1550 time to fit residues: 49.9367 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 : 0.890 ------------------------------------------------------------------------------- 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: 0.0170 chunk 23 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 526 GLN C 417 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.032433 restraints weight = 191849.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.033121 restraints weight = 140723.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.033670 restraints weight = 110770.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.034038 restraints weight = 90972.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034403 restraints weight = 78170.202| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 21879 Z= 0.140 Angle : 0.697 14.524 29696 Z= 0.354 Chirality : 0.042 0.341 3530 Planarity : 0.005 0.070 3801 Dihedral : 11.077 88.911 3397 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.62 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 aren not related in a simple way. whole: 0.67 (0.16), residues: 2857 helix: 1.02 (0.13), residues: 1532 sheet: 1.26 (0.25), residues: 378 loop : -0.78 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 516 TYR 0.011 0.001 TYR C 499 PHE 0.026 0.001 PHE F 231 TRP 0.007 0.001 TRP F 510 HIS 0.007 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00305 (21839) covalent geometry : angle 0.69681 (29696) hydrogen bonds : bond 0.03775 ( 1139) hydrogen bonds : angle 5.15072 ( 3381) Misc. bond : bond 0.00383 ( 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 205 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.877 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: A 271 ARG cc_start: 0.8783 (ptp-110) cc_final: 0.8543 (ptp-170) REVERT: A 384 LEU cc_start: 0.9057 (mt) cc_final: 0.8852 (mt) REVERT: A 552 LEU cc_start: 0.9589 (tt) cc_final: 0.9278 (mt) REVERT: B 368 LEU cc_start: 0.8909 (pp) cc_final: 0.8526 (mm) REVERT: B 370 ILE cc_start: 0.9027 (pt) cc_final: 0.8758 (tp) REVERT: B 573 MET cc_start: 0.8894 (ptp) cc_final: 0.8548 (ptp) REVERT: B 587 LYS cc_start: 0.9148 (ptmm) cc_final: 0.8899 (pptt) REVERT: C 599 CYS cc_start: 0.9135 (t) cc_final: 0.8868 (t) REVERT: C 639 LYS cc_start: 0.9081 (mttp) cc_final: 0.8644 (mmtt) REVERT: C 657 MET cc_start: 0.9024 (mmp) cc_final: 0.8742 (mmm) REVERT: D 354 LEU cc_start: 0.9214 (mm) cc_final: 0.8958 (pp) REVERT: D 583 GLN cc_start: 0.8632 (mp10) cc_final: 0.8407 (mm-40) REVERT: D 593 TYR cc_start: 0.8109 (m-10) cc_final: 0.7845 (m-80) REVERT: D 603 ASP cc_start: 0.8458 (t0) cc_final: 0.8088 (t0) REVERT: D 657 MET cc_start: 0.9069 (ttp) cc_final: 0.8608 (ptt) REVERT: D 709 LYS cc_start: 0.9516 (mmmt) cc_final: 0.9234 (mmmt) REVERT: E 655 MET cc_start: 0.8790 (mpp) cc_final: 0.8117 (mpp) REVERT: E 657 MET cc_start: 0.9279 (mmt) cc_final: 0.8930 (mmm) REVERT: E 712 MET cc_start: 0.9413 (tpt) cc_final: 0.8901 (mtp) REVERT: F 504 MET cc_start: 0.8958 (pmm) cc_final: 0.8741 (pmm) REVERT: F 720 MET cc_start: 0.9211 (mmp) cc_final: 0.8903 (mmp) REVERT: F 724 TYR cc_start: 0.8955 (m-80) cc_final: 0.8698 (m-80) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1390 time to fit residues: 46.0577 Evaluate side-chains 173 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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: 40.0000 chunk 277 optimal weight: 0.0170 chunk 138 optimal weight: 0.0270 chunk 22 optimal weight: 30.0000 chunk 188 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN B 526 GLN D 526 GLN D 530 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.032737 restraints weight = 191875.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.033434 restraints weight = 142337.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.033979 restraints weight = 111779.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.034397 restraints weight = 92036.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.034716 restraints weight = 78788.517| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 21879 Z= 0.136 Angle : 0.693 9.796 29696 Z= 0.353 Chirality : 0.042 0.296 3530 Planarity : 0.005 0.067 3801 Dihedral : 10.910 89.316 3397 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.55 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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 aren not related in a simple way. whole: 0.66 (0.16), residues: 2857 helix: 1.06 (0.13), residues: 1530 sheet: 1.20 (0.25), residues: 378 loop : -0.83 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 315 TYR 0.023 0.001 TYR F 259 PHE 0.022 0.001 PHE A 231 TRP 0.009 0.001 TRP F 510 HIS 0.006 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00293 (21839) covalent geometry : angle 0.69259 (29696) hydrogen bonds : bond 0.03703 ( 1139) hydrogen bonds : angle 5.09421 ( 3381) Misc. bond : bond 0.00362 ( 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 208 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.879 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: A 271 ARG cc_start: 0.8767 (ptp-110) cc_final: 0.8551 (ptp-170) REVERT: A 552 LEU cc_start: 0.9548 (tt) cc_final: 0.9288 (mt) REVERT: A 573 MET cc_start: 0.8758 (mpp) cc_final: 0.8546 (mpp) REVERT: B 368 LEU cc_start: 0.8871 (pp) cc_final: 0.8474 (mm) REVERT: B 370 ILE cc_start: 0.9091 (pt) cc_final: 0.8829 (tp) REVERT: B 587 LYS cc_start: 0.9145 (ptmm) cc_final: 0.8882 (pptt) REVERT: B 657 MET cc_start: 0.9031 (tpp) cc_final: 0.8621 (tpp) REVERT: C 304 LYS cc_start: 0.9352 (pptt) cc_final: 0.9025 (pttp) REVERT: C 599 CYS cc_start: 0.9061 (t) cc_final: 0.8859 (t) REVERT: C 639 LYS cc_start: 0.9044 (mttp) cc_final: 0.8596 (mmtt) REVERT: C 657 MET cc_start: 0.9206 (mmp) cc_final: 0.8975 (mmm) REVERT: D 354 LEU cc_start: 0.9233 (mm) cc_final: 0.8981 (pp) REVERT: D 453 MET cc_start: 0.9166 (mmp) cc_final: 0.8829 (mtt) REVERT: D 590 ASP cc_start: 0.9030 (m-30) cc_final: 0.8632 (m-30) REVERT: D 593 TYR cc_start: 0.8155 (m-10) cc_final: 0.7877 (m-80) REVERT: D 599 CYS cc_start: 0.8717 (t) cc_final: 0.8486 (t) REVERT: D 603 ASP cc_start: 0.8365 (t0) cc_final: 0.7888 (t0) REVERT: D 657 MET cc_start: 0.9069 (ttp) cc_final: 0.8686 (ptt) REVERT: D 709 LYS cc_start: 0.9524 (mmmt) cc_final: 0.9258 (mmmt) REVERT: E 585 MET cc_start: 0.9260 (tpt) cc_final: 0.9006 (tpt) REVERT: E 657 MET cc_start: 0.9320 (mmt) cc_final: 0.8980 (mmm) REVERT: E 712 MET cc_start: 0.9452 (tpt) cc_final: 0.8906 (mtp) REVERT: E 720 MET cc_start: 0.8419 (tpp) cc_final: 0.7993 (tpt) REVERT: F 504 MET cc_start: 0.8909 (pmm) cc_final: 0.8660 (pmm) REVERT: F 657 MET cc_start: 0.8932 (mmp) cc_final: 0.8722 (mmm) REVERT: F 720 MET cc_start: 0.9153 (mmp) cc_final: 0.8614 (mmm) REVERT: F 724 TYR cc_start: 0.8996 (m-80) cc_final: 0.8744 (m-80) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1341 time to fit residues: 44.3699 Evaluate side-chains 172 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 5.9990 chunk 242 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 526 GLN D 408 HIS ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN E 374 ASN ** 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 = 0.3146 r_free = 0.3146 target = 0.042863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.031473 restraints weight = 198783.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032132 restraints weight = 145703.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.032648 restraints weight = 114632.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033061 restraints weight = 94350.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033349 restraints weight = 80295.154| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 21879 Z= 0.204 Angle : 0.740 17.439 29696 Z= 0.382 Chirality : 0.043 0.328 3530 Planarity : 0.005 0.073 3801 Dihedral : 11.021 87.887 3397 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.25 % Favored : 94.22 % Rotamer: Outliers : 0.05 % Allowed : 0.91 % Favored : 99.04 % 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 aren not related in a simple way. whole: 0.44 (0.16), residues: 2857 helix: 0.91 (0.13), residues: 1548 sheet: 0.91 (0.25), residues: 376 loop : -0.92 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 315 TYR 0.017 0.002 TYR D 611 PHE 0.022 0.002 PHE A 231 TRP 0.018 0.002 TRP D 510 HIS 0.007 0.001 HIS B 546 Details of bonding type rmsd covalent geometry : bond 0.00432 (21839) covalent geometry : angle 0.74026 (29696) hydrogen bonds : bond 0.03935 ( 1139) hydrogen bonds : angle 5.35373 ( 3381) Misc. bond : bond 0.00375 ( 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 195 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.933 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: A 271 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.8574 (ptp-170) REVERT: A 552 LEU cc_start: 0.9548 (tt) cc_final: 0.9326 (mt) REVERT: A 573 MET cc_start: 0.8756 (mpp) cc_final: 0.8495 (mpp) REVERT: B 368 LEU cc_start: 0.8887 (pp) cc_final: 0.8492 (mm) REVERT: B 573 MET cc_start: 0.8951 (ptp) cc_final: 0.8639 (ptp) REVERT: B 654 GLU cc_start: 0.8995 (pt0) cc_final: 0.8743 (pp20) REVERT: B 655 MET cc_start: 0.8626 (mmp) cc_final: 0.7616 (mmt) REVERT: B 657 MET cc_start: 0.9062 (tpp) cc_final: 0.8788 (tpp) REVERT: C 639 LYS cc_start: 0.9089 (mttp) cc_final: 0.8625 (mmtt) REVERT: C 657 MET cc_start: 0.9181 (mmp) cc_final: 0.8963 (mmm) REVERT: D 354 LEU cc_start: 0.9190 (mm) cc_final: 0.8931 (pp) REVERT: D 372 MET cc_start: 0.6276 (ttm) cc_final: 0.6070 (tmm) REVERT: D 585 MET cc_start: 0.9361 (mmp) cc_final: 0.9140 (mmm) REVERT: D 593 TYR cc_start: 0.8286 (m-10) cc_final: 0.7893 (m-80) REVERT: D 603 ASP cc_start: 0.8525 (t0) cc_final: 0.8192 (t0) REVERT: D 657 MET cc_start: 0.9060 (ttp) cc_final: 0.8622 (ptt) REVERT: E 657 MET cc_start: 0.9305 (mmt) cc_final: 0.8938 (mmm) REVERT: E 712 MET cc_start: 0.9454 (tpt) cc_final: 0.8957 (mtp) REVERT: E 720 MET cc_start: 0.8442 (tpp) cc_final: 0.7898 (tpt) REVERT: F 372 MET cc_start: 0.4833 (ppp) cc_final: 0.4603 (tpp) REVERT: F 504 MET cc_start: 0.9044 (pmm) cc_final: 0.8812 (pmm) REVERT: F 712 MET cc_start: 0.8675 (ppp) cc_final: 0.8280 (ppp) REVERT: F 720 MET cc_start: 0.9269 (mmp) cc_final: 0.9041 (mmp) REVERT: F 724 TYR cc_start: 0.8992 (m-80) cc_final: 0.8743 (m-80) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1307 time to fit residues: 40.9447 Evaluate side-chains 157 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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: 8.9990 chunk 228 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 250 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 244 optimal weight: 20.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN B 526 GLN C 505 ASN 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 = 0.3149 r_free = 0.3149 target = 0.042975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.031534 restraints weight = 196739.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032214 restraints weight = 144309.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.032762 restraints weight = 112509.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033163 restraints weight = 92309.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.033456 restraints weight = 78801.767| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 21879 Z= 0.170 Angle : 0.734 15.789 29696 Z= 0.374 Chirality : 0.043 0.316 3530 Planarity : 0.005 0.067 3801 Dihedral : 11.055 86.476 3397 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.97 % Favored : 94.54 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % Favored : 99.62 % 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 aren not related in a simple way. whole: 0.45 (0.16), residues: 2857 helix: 0.94 (0.13), residues: 1536 sheet: 0.80 (0.25), residues: 378 loop : -0.90 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 607 TYR 0.016 0.001 TYR F 259 PHE 0.022 0.002 PHE A 231 TRP 0.008 0.001 TRP D 510 HIS 0.008 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00369 (21839) covalent geometry : angle 0.73350 (29696) hydrogen bonds : bond 0.03901 ( 1139) hydrogen bonds : angle 5.31805 ( 3381) Misc. bond : bond 0.00393 ( 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 192 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.892 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: 0.8849 (ptp-110) cc_final: 0.8614 (ptp-170) REVERT: A 552 LEU cc_start: 0.9533 (tt) cc_final: 0.9322 (mt) REVERT: A 573 MET cc_start: 0.8870 (mpp) cc_final: 0.8647 (mpp) REVERT: B 368 LEU cc_start: 0.8881 (pp) cc_final: 0.8500 (mm) REVERT: B 573 MET cc_start: 0.8909 (ptp) cc_final: 0.8573 (ptp) REVERT: B 655 MET cc_start: 0.8536 (mmp) cc_final: 0.7589 (mmt) REVERT: C 639 LYS cc_start: 0.9097 (mttp) cc_final: 0.8616 (mmtt) REVERT: C 657 MET cc_start: 0.9223 (mmp) cc_final: 0.9012 (mmm) REVERT: D 453 MET cc_start: 0.9216 (mmp) cc_final: 0.8978 (mtt) REVERT: D 504 MET cc_start: 0.8842 (mmp) cc_final: 0.8638 (mpp) REVERT: D 603 ASP cc_start: 0.8577 (t0) cc_final: 0.8210 (t0) REVERT: D 657 MET cc_start: 0.9062 (ttp) cc_final: 0.8547 (ptt) REVERT: E 657 MET cc_start: 0.9366 (mmt) cc_final: 0.9142 (mmm) REVERT: E 712 MET cc_start: 0.9452 (tpt) cc_final: 0.8950 (mtp) REVERT: E 720 MET cc_start: 0.8419 (tpp) cc_final: 0.7861 (tpp) REVERT: F 372 MET cc_start: 0.4828 (ppp) cc_final: 0.4595 (tpp) REVERT: F 504 MET cc_start: 0.8986 (pmm) cc_final: 0.8701 (pmm) REVERT: F 720 MET cc_start: 0.9251 (mmp) cc_final: 0.8939 (mmp) REVERT: F 724 TYR cc_start: 0.8995 (m-80) cc_final: 0.8732 (m-80) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1404 time to fit residues: 43.6422 Evaluate side-chains 158 residues out of total 2481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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: 30.0000 chunk 158 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 0.0060 chunk 173 optimal weight: 4.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN B 526 GLN ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.042670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.031214 restraints weight = 197725.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.031894 restraints weight = 143857.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.032414 restraints weight = 112580.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.032788 restraints weight = 92482.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.033103 restraints weight = 78933.152| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21879 Z= 0.173 Angle : 0.727 14.191 29696 Z= 0.372 Chirality : 0.043 0.297 3530 Planarity : 0.005 0.071 3801 Dihedral : 11.050 89.782 3397 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.29 % Favored : 94.19 % Rotamer: Outliers : 0.05 % Allowed : 0.67 % Favored : 99.28 % 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 aren not related in a simple way. whole: 0.38 (0.16), residues: 2857 helix: 0.92 (0.13), residues: 1544 sheet: 0.63 (0.25), residues: 378 loop : -0.94 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 607 TYR 0.012 0.001 TYR E 502 PHE 0.022 0.002 PHE A 231 TRP 0.009 0.001 TRP E 510 HIS 0.008 0.001 HIS F 546 Details of bonding type rmsd covalent geometry : bond 0.00376 (21839) covalent geometry : angle 0.72681 (29696) hydrogen bonds : bond 0.03882 ( 1139) hydrogen bonds : angle 5.37112 ( 3381) Misc. bond : bond 0.00383 ( 40) =============================================================================== Job complete usr+sys time: 4123.99 seconds wall clock time: 71 minutes 57.96 seconds (4317.96 seconds total)