Starting phenix.real_space_refine on Sun Jul 5 08:37:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t3i_25659/07_2026/7t3i_25659.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3i_25659/07_2026/7t3i_25659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7t3i_25659/07_2026/7t3i_25659.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t3i_25659/07_2026/7t3i_25659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t3i_25659/07_2026/7t3i_25659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3i_25659/07_2026/7t3i_25659.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3i_25659/07_2026/7t3i_25659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3i_25659/07_2026/7t3i_25659.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 25 5.49 5 S 123 5.16 5 C 16704 2.51 5 N 4786 2.21 5 O 5161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26799 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4437 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 545} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4443 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4433 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4443 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 4412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4412 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 542} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4243 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'ATP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.43, per 1000 atoms: 0.24 Number of scatterers: 26799 At special positions: 0 Unit cell: (151.152, 145.904, 117.563, 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 123 16.00 P 25 15.00 O 5161 8.00 N 4786 7.00 C 16704 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 Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6432 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 12 sheets defined 59.9% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.987A pdb=" N LYS A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.937A pdb=" N ILE A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 removed outlier: 4.286A pdb=" N ARG A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 438 removed outlier: 4.139A pdb=" N ALA A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.723A pdb=" N HIS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.606A pdb=" N SER A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.596A pdb=" N ILE A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.778A pdb=" N PHE A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.646A pdb=" N LYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 removed outlier: 3.759A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 618 through 632 Processing helix chain 'A' and resid 670 through 684 removed outlier: 3.865A pdb=" N VAL A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 725 through 729 removed outlier: 3.760A pdb=" N THR A 729 " --> pdb=" O LEU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 776 through 786 removed outlier: 4.045A pdb=" N TRP A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 781 " --> pdb=" O MET A 777 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 799 removed outlier: 3.854A pdb=" N TYR A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 207 through 224 removed outlier: 4.740A pdb=" N PHE B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 248 through 261 removed outlier: 3.628A pdb=" N HIS B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.873A pdb=" N VAL B 272 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 273 " --> pdb=" O PRO B 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 273' Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 303 through 308 removed outlier: 4.315A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 337 removed outlier: 3.866A pdb=" N ASP B 331 " --> pdb=" O MET B 327 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.776A pdb=" N ARG B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.506A pdb=" N MET B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 438 removed outlier: 4.529A pdb=" N ALA B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.535A pdb=" N ALA B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.568A pdb=" N SER B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.554A pdb=" N PHE B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.871A pdb=" N LYS B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 593 removed outlier: 3.664A pdb=" N SER B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 581 " --> pdb=" O GLY B 577 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.840A pdb=" N LEU B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 631 removed outlier: 3.511A pdb=" N ARG B 620 " --> pdb=" O ASP B 616 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 removed outlier: 3.665A pdb=" N ILE B 650 " --> pdb=" O PRO B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 684 removed outlier: 4.099A pdb=" N VAL B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 732 through 762 removed outlier: 3.510A pdb=" N GLY B 737 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 785 removed outlier: 3.917A pdb=" N TRP B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 798 Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 207 through 224 removed outlier: 3.661A pdb=" N LYS C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 248 through 261 Processing helix chain 'C' and resid 270 through 273 Processing helix chain 'C' and resid 278 through 294 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 316 through 337 removed outlier: 3.731A pdb=" N SER C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 331 " --> pdb=" O MET C 327 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.590A pdb=" N PHE C 354 " --> pdb=" O ARG C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 removed outlier: 3.560A pdb=" N ARG C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.861A pdb=" N LEU C 399 " --> pdb=" O ASN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 438 removed outlier: 4.027A pdb=" N ALA C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 428 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 460 Processing helix chain 'C' and resid 472 through 481 removed outlier: 3.525A pdb=" N PHE C 476 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 removed outlier: 3.572A pdb=" N GLU C 490 " --> pdb=" O SER C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 517 through 523 Processing helix chain 'C' and resid 523 through 531 removed outlier: 3.560A pdb=" N PHE C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 3.959A pdb=" N LYS C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 593 removed outlier: 3.764A pdb=" N SER C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 580 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 583 " --> pdb=" O SER C 579 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 592 " --> pdb=" O SER C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 631 Processing helix chain 'C' and resid 670 through 686 removed outlier: 4.091A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 685 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 724 Processing helix chain 'C' and resid 725 through 729 removed outlier: 3.717A pdb=" N THR C 729 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 762 removed outlier: 3.828A pdb=" N GLY C 737 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 785 Processing helix chain 'C' and resid 794 through 799 removed outlier: 3.908A pdb=" N HIS C 799 " --> pdb=" O GLU C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 207 through 224 removed outlier: 4.042A pdb=" N LYS D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.547A pdb=" N CYS D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 removed outlier: 3.593A pdb=" N HIS D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.884A pdb=" N VAL D 272 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 294 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.943A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 337 removed outlier: 4.162A pdb=" N SER D 320 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP D 331 " --> pdb=" O MET D 327 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.809A pdb=" N ARG D 361 " --> pdb=" O PRO D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.746A pdb=" N GLN D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 removed outlier: 4.151A pdb=" N LEU D 399 " --> pdb=" O ASN D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 438 removed outlier: 4.130A pdb=" N ALA D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 460 removed outlier: 3.635A pdb=" N HIS D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.743A pdb=" N SER D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 506 through 517 Processing helix chain 'D' and resid 517 through 523 Processing helix chain 'D' and resid 523 through 531 removed outlier: 3.569A pdb=" N PHE D 527 " --> pdb=" O ASN D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.504A pdb=" N LYS D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 593 removed outlier: 3.899A pdb=" N SER D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 607 removed outlier: 4.132A pdb=" N LEU D 606 " --> pdb=" O GLN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 631 removed outlier: 4.100A pdb=" N ARG D 620 " --> pdb=" O ASP D 616 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 650 removed outlier: 3.854A pdb=" N ILE D 650 " --> pdb=" O PRO D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 684 removed outlier: 3.876A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 724 Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 732 through 762 removed outlier: 3.720A pdb=" N GLY D 737 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS D 758 " --> pdb=" O GLN D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 784 removed outlier: 3.566A pdb=" N TRP D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 797 Processing helix chain 'E' and resid 200 through 204 Processing helix chain 'E' and resid 207 through 218 removed outlier: 3.884A pdb=" N ARG E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.520A pdb=" N ARG E 223 " --> pdb=" O TRP E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 248 through 261 Processing helix chain 'E' and resid 270 through 273 Processing helix chain 'E' and resid 279 through 294 Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 316 through 336 removed outlier: 3.994A pdb=" N SER E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 356 through 363 removed outlier: 3.783A pdb=" N PHE E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 407 through 438 removed outlier: 3.779A pdb=" N ALA E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 460 removed outlier: 3.508A pdb=" N LEU E 455 " --> pdb=" O ARG E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 removed outlier: 3.783A pdb=" N PHE E 476 " --> pdb=" O THR E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 506 through 517 Processing helix chain 'E' and resid 517 through 523 Processing helix chain 'E' and resid 523 through 531 removed outlier: 3.603A pdb=" N VAL E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 560 Processing helix chain 'E' and resid 568 through 572 removed outlier: 4.464A pdb=" N LEU E 571 " --> pdb=" O GLY E 568 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 572 " --> pdb=" O PRO E 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 568 through 572' Processing helix chain 'E' and resid 577 through 593 removed outlier: 3.538A pdb=" N ALA E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 606 Processing helix chain 'E' and resid 616 through 632 removed outlier: 3.590A pdb=" N VAL E 621 " --> pdb=" O ALA E 617 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR E 624 " --> pdb=" O ARG E 620 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 632 " --> pdb=" O GLU E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 650 Processing helix chain 'E' and resid 672 through 684 removed outlier: 4.469A pdb=" N LYS E 676 " --> pdb=" O GLU E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 715 through 724 removed outlier: 3.711A pdb=" N LEU E 719 " --> pdb=" O THR E 715 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E 720 " --> pdb=" O ASP E 716 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 756 removed outlier: 3.529A pdb=" N GLN E 756 " --> pdb=" O TYR E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 776 through 786 removed outlier: 3.825A pdb=" N TRP E 780 " --> pdb=" O THR E 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 Processing helix chain 'F' and resid 207 through 223 removed outlier: 4.597A pdb=" N LYS F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Proline residue: F 221 - end of helix Processing helix chain 'F' and resid 224 through 232 removed outlier: 4.352A pdb=" N CYS F 228 " --> pdb=" O GLY F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 261 removed outlier: 3.810A pdb=" N GLY F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 294 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 319 through 337 Processing helix chain 'F' and resid 351 through 355 Processing helix chain 'F' and resid 356 through 363 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 402 removed outlier: 3.947A pdb=" N LEU F 399 " --> pdb=" O ASN F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 438 removed outlier: 3.504A pdb=" N ALA F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN F 426 " --> pdb=" O SER F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 460 removed outlier: 3.579A pdb=" N HIS F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 483 removed outlier: 3.698A pdb=" N SER F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 482 " --> pdb=" O LYS F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 517 Processing helix chain 'F' and resid 517 through 523 Processing helix chain 'F' and resid 523 through 531 removed outlier: 3.807A pdb=" N PHE F 527 " --> pdb=" O ASN F 523 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR F 528 " --> pdb=" O PRO F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 560 Processing helix chain 'F' and resid 576 through 593 removed outlier: 4.235A pdb=" N GLU F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG F 581 " --> pdb=" O GLY F 577 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 583 " --> pdb=" O SER F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 606 Processing helix chain 'F' and resid 615 through 632 removed outlier: 3.686A pdb=" N VAL F 632 " --> pdb=" O GLU F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 650 removed outlier: 3.603A pdb=" N MET F 649 " --> pdb=" O ARG F 646 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE F 650 " --> pdb=" O PRO F 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 646 through 650' Processing helix chain 'F' and resid 651 through 656 removed outlier: 4.134A pdb=" N ARG F 655 " --> pdb=" O ASP F 651 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG F 656 " --> pdb=" O GLU F 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 651 through 656' Processing helix chain 'F' and resid 670 through 685 removed outlier: 3.502A pdb=" N LYS F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 724 Processing helix chain 'F' and resid 732 through 761 removed outlier: 4.101A pdb=" N GLY F 737 " --> pdb=" O GLY F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 776 through 787 Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.775A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 267 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY A 238 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 367 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 240 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 567 removed outlier: 3.501A pdb=" N ASP A 601 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 643 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ILE A 664 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 539 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 263 through 267 removed outlier: 3.557A pdb=" N PHE B 300 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 562 through 566 removed outlier: 3.565A pdb=" N ASP B 601 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 643 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B 662 " --> pdb=" O GLY B 537 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 539 " --> pdb=" O THR B 662 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 268 removed outlier: 3.614A pdb=" N PHE C 300 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 302 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY C 238 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE C 367 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C 240 " --> pdb=" O ILE C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 562 through 567 removed outlier: 6.820A pdb=" N ASN C 562 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE C 599 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 564 " --> pdb=" O PHE C 599 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP C 601 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 566 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR C 662 " --> pdb=" O GLY C 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 267 removed outlier: 4.010A pdb=" N PHE D 300 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 365 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 562 through 567 removed outlier: 7.247A pdb=" N ASN D 562 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE D 599 " --> pdb=" O ASN D 562 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 564 " --> pdb=" O PHE D 599 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP D 601 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 566 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 538 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY D 537 " --> pdb=" O THR D 662 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE D 664 " --> pdb=" O GLY D 537 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU D 539 " --> pdb=" O ILE D 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.825A pdb=" N ALA E 263 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE E 300 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 265 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP E 302 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL E 267 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 349 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL E 365 " --> pdb=" O GLY E 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 562 through 565 removed outlier: 7.014A pdb=" N ILE E 538 " --> pdb=" O GLY E 642 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR E 662 " --> pdb=" O GLY E 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 264 through 267 removed outlier: 6.504A pdb=" N ILE F 265 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP F 302 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL F 267 " --> pdb=" O ASP F 302 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N CYS F 297 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU F 346 " --> pdb=" O CYS F 297 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE F 299 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ALA F 348 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU F 301 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL F 239 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR F 349 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU F 241 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 365 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS F 242 " --> pdb=" O ILE F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 562 through 566 removed outlier: 6.048A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS F 596 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE F 641 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 598 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA F 643 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE F 600 " --> pdb=" O ALA F 643 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE F 538 " --> pdb=" O GLY F 642 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ILE F 664 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU F 539 " --> pdb=" O ILE F 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1308 hydrogen bonds defined for protein. 3753 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: 4.97 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9127 1.34 - 1.46: 5386 1.46 - 1.58: 12492 1.58 - 1.70: 32 1.70 - 1.82: 205 Bond restraints: 27242 Sorted by residual: bond pdb=" O3 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" O4 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" O2 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.46e+00 bond pdb=" O1 PO4 E 901 " pdb=" P PO4 E 901 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.05e+00 ... (remaining 27237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 36495 2.40 - 4.81: 371 4.81 - 7.21: 27 7.21 - 9.61: 4 9.61 - 12.01: 3 Bond angle restraints: 36900 Sorted by residual: angle pdb=" CA LEU C 660 " pdb=" CB LEU C 660 " pdb=" CG LEU C 660 " ideal model delta sigma weight residual 116.30 128.31 -12.01 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sigma weight residual 112.00 107.46 4.54 1.40e+00 5.10e-01 1.05e+01 angle pdb=" CG ARG B 321 " pdb=" CD ARG B 321 " pdb=" NE ARG B 321 " ideal model delta sigma weight residual 112.00 119.06 -7.06 2.20e+00 2.07e-01 1.03e+01 angle pdb=" C GLU F 217 " pdb=" N VAL F 218 " pdb=" CA VAL F 218 " ideal model delta sigma weight residual 123.16 119.86 3.30 1.06e+00 8.90e-01 9.70e+00 angle pdb=" N ILE F 654 " pdb=" CA ILE F 654 " pdb=" C ILE F 654 " ideal model delta sigma weight residual 111.90 109.41 2.49 8.10e-01 1.52e+00 9.41e+00 ... (remaining 36895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 15361 18.01 - 36.02: 1157 36.02 - 54.03: 132 54.03 - 72.04: 28 72.04 - 90.05: 16 Dihedral angle restraints: 16694 sinusoidal: 6761 harmonic: 9933 Sorted by residual: dihedral pdb=" CA GLU E 770 " pdb=" C GLU E 770 " pdb=" N ILE E 771 " pdb=" CA ILE E 771 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA THR F 494 " pdb=" C THR F 494 " pdb=" N ILE F 495 " pdb=" CA ILE F 495 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLU C 570 " pdb=" C GLU C 570 " pdb=" N LEU C 571 " pdb=" CA LEU C 571 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 16691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2880 0.036 - 0.072: 946 0.072 - 0.108: 296 0.108 - 0.144: 69 0.144 - 0.180: 5 Chirality restraints: 4196 Sorted by residual: chirality pdb=" CA GLN F 448 " pdb=" N GLN F 448 " pdb=" C GLN F 448 " pdb=" CB GLN F 448 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA GLN C 448 " pdb=" N GLN C 448 " pdb=" C GLN C 448 " pdb=" CB GLN C 448 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA VAL B 407 " pdb=" N VAL B 407 " pdb=" C VAL B 407 " pdb=" CB VAL B 407 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 4193 not shown) Planarity restraints: 4790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 484 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 485 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 484 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 485 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 485 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 485 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 356 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO F 357 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.029 5.00e-02 4.00e+02 ... (remaining 4787 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 446 2.66 - 3.22: 26285 3.22 - 3.78: 41214 3.78 - 4.34: 53653 4.34 - 4.90: 86222 Nonbonded interactions: 207820 Sorted by model distance: nonbonded pdb=" OG SER D 732 " pdb=" OD1 ASP D 735 " model vdw 2.101 3.040 nonbonded pdb=" OH TYR F 406 " pdb=" O VAL F 483 " model vdw 2.176 3.040 nonbonded pdb=" O TYR D 235 " pdb=" ND2 ASN D 342 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASN B 237 " pdb=" OG SER B 364 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR B 797 " pdb=" OE1 GLU C 652 " model vdw 2.219 3.040 ... (remaining 207815 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 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 460 or (resid 461 through 463 and (name N or nam \ e CA or name C or name O or name CB )) or resid 464 through 686 or resid 713 thr \ ough 761 or resid 770 through 790)) selection = (chain 'B' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'C' and (resid 199 through 272 or resid 277 through 309 or resid 318 thro \ ugh 460 or (resid 461 through 463 and (name N or name CA or name C or name O or \ name CB )) or resid 464 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'D' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'E' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 272 or resid 277 t \ hrough 309 or resid 318 through 686 or resid 713 through 761 or resid 768 or res \ id 771 through 790)) selection = (chain 'F' and (resid 199 through 225 or (resid 226 through 230 and (name N or n \ ame CA or name C or name O or name CB )) or resid 231 through 460 or (resid 461 \ through 463 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 4 through 761 or resid 770 through 790)) } 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.980 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.003 0.087 27244 Z= 0.124 Angle : 0.587 12.015 36900 Z= 0.316 Chirality : 0.041 0.180 4196 Planarity : 0.004 0.067 4790 Dihedral : 12.509 90.047 10262 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.71 % Favored : 94.05 % Rotamer: Outliers : 0.07 % Allowed : 0.18 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3397 helix: 1.34 (0.13), residues: 1717 sheet: 0.05 (0.28), residues: 342 loop : -0.73 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 351 TYR 0.035 0.001 TYR D 752 PHE 0.017 0.001 PHE A 731 TRP 0.018 0.001 TRP B 453 HIS 0.002 0.000 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (27242) covalent geometry : angle 0.58666 / 0.32 (36900) hydrogen bonds : bond 0.18431 / 12.64 ( 1308) hydrogen bonds : angle 5.90610 / 4.29 ( 3753) Misc. bond : bond 0.00052 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 449 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.9157 (tp) cc_final: 0.8777 (tt) REVERT: B 546 CYS cc_start: 0.8744 (m) cc_final: 0.8208 (m) REVERT: B 585 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8364 (tm-30) REVERT: C 318 MET cc_start: 0.9066 (tmm) cc_final: 0.8711 (tmm) REVERT: C 368 ASP cc_start: 0.8665 (t70) cc_final: 0.8241 (t0) REVERT: C 369 MET cc_start: 0.8571 (ptm) cc_final: 0.8348 (ppp) REVERT: C 473 MET cc_start: 0.7722 (tpt) cc_final: 0.7405 (tpp) REVERT: C 574 LYS cc_start: 0.8903 (ptmt) cc_final: 0.8683 (ptmt) REVERT: D 204 ILE cc_start: 0.9122 (tt) cc_final: 0.8914 (pt) REVERT: D 281 GLU cc_start: 0.8927 (mp0) cc_final: 0.8467 (mp0) REVERT: D 416 LYS cc_start: 0.9044 (tppt) cc_final: 0.8427 (tppt) REVERT: D 740 MET cc_start: 0.7721 (tmm) cc_final: 0.7381 (tmm) REVERT: E 304 ILE cc_start: 0.9306 (tp) cc_final: 0.9096 (tp) REVERT: E 473 MET cc_start: 0.8619 (tpt) cc_final: 0.8349 (mmm) REVERT: E 515 MET cc_start: 0.8705 (tpp) cc_final: 0.8177 (tpp) REVERT: E 630 ASP cc_start: 0.7795 (t0) cc_final: 0.7308 (t0) REVERT: F 219 TRP cc_start: 0.5802 (t-100) cc_final: 0.5575 (t-100) REVERT: F 303 GLU cc_start: 0.6467 (mp0) cc_final: 0.5972 (mp0) REVERT: F 371 MET cc_start: 0.6999 (tmm) cc_final: 0.6643 (tmm) REVERT: F 745 GLN cc_start: 0.8713 (mt0) cc_final: 0.8309 (mt0) outliers start: 2 outliers final: 0 residues processed: 450 average time/residue: 0.1537 time to fit residues: 113.7839 Evaluate side-chains 322 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 5.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN B 242 HIS B 426 ASN B 459 HIS C 328 ASN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN D 585 GLN E 342 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.100553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079634 restraints weight = 69724.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.081769 restraints weight = 42102.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.083264 restraints weight = 29146.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084287 restraints weight = 22186.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084875 restraints weight = 18246.639| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27244 Z= 0.122 Angle : 0.556 8.808 36900 Z= 0.286 Chirality : 0.041 0.160 4196 Planarity : 0.005 0.054 4790 Dihedral : 4.470 58.323 3776 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.30 % Favored : 94.47 % Rotamer: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3397 helix: 1.34 (0.12), residues: 1784 sheet: -0.13 (0.27), residues: 364 loop : -0.67 (0.19), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.022 0.001 TYR D 413 PHE 0.016 0.002 PHE E 264 TRP 0.026 0.001 TRP B 219 HIS 0.004 0.001 HIS E 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (27242) covalent geometry : angle 0.55623 / 0.29 (36900) hydrogen bonds : bond 0.04141 / 2.81 ( 1308) hydrogen bonds : angle 4.58055 / 3.38 ( 3753) Misc. bond : bond 0.00027 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 423 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.8658 (m-30) cc_final: 0.7995 (p0) REVERT: A 518 ILE cc_start: 0.9387 (mt) cc_final: 0.9156 (tp) REVERT: A 522 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8472 (ptmt) REVERT: A 539 LEU cc_start: 0.9482 (tp) cc_final: 0.9256 (tt) REVERT: A 546 CYS cc_start: 0.8793 (m) cc_final: 0.8438 (m) REVERT: A 728 CYS cc_start: 0.7623 (t) cc_final: 0.7339 (t) REVERT: B 320 SER cc_start: 0.9256 (t) cc_final: 0.8832 (m) REVERT: B 327 MET cc_start: 0.8588 (tpp) cc_final: 0.8171 (tpt) REVERT: B 395 ASN cc_start: 0.9146 (t0) cc_final: 0.8910 (t0) REVERT: B 401 LYS cc_start: 0.9172 (mttt) cc_final: 0.8855 (tppt) REVERT: B 546 CYS cc_start: 0.8647 (m) cc_final: 0.8151 (m) REVERT: B 740 MET cc_start: 0.8671 (tmm) cc_final: 0.8363 (tmm) REVERT: C 318 MET cc_start: 0.8682 (tmm) cc_final: 0.8324 (tmm) REVERT: C 368 ASP cc_start: 0.8774 (t70) cc_final: 0.8379 (t0) REVERT: C 473 MET cc_start: 0.7683 (tpt) cc_final: 0.7452 (tpt) REVERT: C 493 SER cc_start: 0.9169 (m) cc_final: 0.8822 (p) REVERT: C 538 ILE cc_start: 0.8999 (pt) cc_final: 0.8795 (mm) REVERT: C 574 LYS cc_start: 0.8904 (ptmt) cc_final: 0.8612 (ptmt) REVERT: C 652 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 741 GLN cc_start: 0.8391 (tp40) cc_final: 0.8060 (tp40) REVERT: D 204 ILE cc_start: 0.9082 (tt) cc_final: 0.8873 (pt) REVERT: D 286 ASP cc_start: 0.7856 (t70) cc_final: 0.7616 (t0) REVERT: D 466 TRP cc_start: 0.6490 (p90) cc_final: 0.6232 (p90) REVERT: D 473 MET cc_start: 0.8250 (mmm) cc_final: 0.8038 (mmm) REVERT: D 580 GLU cc_start: 0.8859 (mp0) cc_final: 0.8476 (mp0) REVERT: D 649 MET cc_start: 0.8166 (tpt) cc_final: 0.7870 (tpp) REVERT: D 740 MET cc_start: 0.7941 (tmm) cc_final: 0.7564 (tmm) REVERT: E 515 MET cc_start: 0.8898 (tpp) cc_final: 0.8324 (tpp) REVERT: E 624 THR cc_start: 0.9552 (p) cc_final: 0.9165 (t) REVERT: E 630 ASP cc_start: 0.7995 (t0) cc_final: 0.7464 (t0) REVERT: F 219 TRP cc_start: 0.5697 (t-100) cc_final: 0.5490 (t-100) REVERT: F 303 GLU cc_start: 0.6477 (mp0) cc_final: 0.5974 (mp0) REVERT: F 371 MET cc_start: 0.7208 (tmm) cc_final: 0.6430 (mmt) REVERT: F 482 LEU cc_start: 0.9042 (mt) cc_final: 0.8820 (tt) REVERT: F 539 LEU cc_start: 0.9435 (tp) cc_final: 0.9073 (mp) REVERT: F 745 GLN cc_start: 0.8701 (mt0) cc_final: 0.8432 (pt0) outliers start: 2 outliers final: 0 residues processed: 424 average time/residue: 0.1603 time to fit residues: 110.5456 Evaluate side-chains 325 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 269 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 294 optimal weight: 20.0000 chunk 64 optimal weight: 0.0970 chunk 125 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 321 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 overall best weight: 4.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN A 585 GLN B 426 ASN B 459 HIS ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 ASN E 342 ASN E 459 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.076480 restraints weight = 70810.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.078514 restraints weight = 43497.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.079889 restraints weight = 30408.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.080830 restraints weight = 23496.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081435 restraints weight = 19506.620| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27244 Z= 0.211 Angle : 0.617 7.697 36900 Z= 0.317 Chirality : 0.042 0.168 4196 Planarity : 0.005 0.053 4790 Dihedral : 4.638 57.184 3776 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.68 % Favored : 93.08 % Rotamer: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3397 helix: 1.25 (0.12), residues: 1813 sheet: -0.29 (0.27), residues: 354 loop : -0.78 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 361 TYR 0.033 0.002 TYR D 752 PHE 0.020 0.002 PHE D 587 TRP 0.014 0.002 TRP C 219 HIS 0.007 0.001 HIS E 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (27242) covalent geometry : angle 0.61705 / 0.32 (36900) hydrogen bonds : bond 0.04035 / 2.74 ( 1308) hydrogen bonds : angle 4.60301 / 3.38 ( 3753) Misc. bond : bond 0.00097 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 401 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8503 (ptmt) REVERT: A 546 CYS cc_start: 0.8808 (m) cc_final: 0.8460 (m) REVERT: A 566 ILE cc_start: 0.9633 (mm) cc_final: 0.9420 (mm) REVERT: B 240 LEU cc_start: 0.8573 (tp) cc_final: 0.7920 (tp) REVERT: B 302 ASP cc_start: 0.8315 (p0) cc_final: 0.7277 (p0) REVERT: B 305 ASP cc_start: 0.8965 (p0) cc_final: 0.8719 (p0) REVERT: B 327 MET cc_start: 0.8620 (tpp) cc_final: 0.8408 (tpt) REVERT: B 395 ASN cc_start: 0.9165 (t0) cc_final: 0.8922 (t0) REVERT: B 401 LYS cc_start: 0.9184 (mttt) cc_final: 0.8865 (tppt) REVERT: B 546 CYS cc_start: 0.8709 (m) cc_final: 0.8279 (m) REVERT: B 740 MET cc_start: 0.8768 (tmm) cc_final: 0.8423 (tmm) REVERT: C 318 MET cc_start: 0.8656 (tmm) cc_final: 0.8319 (tmm) REVERT: C 327 MET cc_start: 0.9223 (tpp) cc_final: 0.9013 (tpp) REVERT: C 369 MET cc_start: 0.8693 (ptm) cc_final: 0.8429 (ptt) REVERT: C 473 MET cc_start: 0.7592 (tpt) cc_final: 0.7275 (tpp) REVERT: C 525 GLU cc_start: 0.8127 (pm20) cc_final: 0.7321 (mt-10) REVERT: C 574 LYS cc_start: 0.8931 (ptmt) cc_final: 0.8637 (ptmt) REVERT: C 596 CYS cc_start: 0.8770 (t) cc_final: 0.8339 (p) REVERT: C 646 ARG cc_start: 0.8684 (ptt90) cc_final: 0.8457 (ptt90) REVERT: C 741 GLN cc_start: 0.8295 (tp40) cc_final: 0.7918 (tp-100) REVERT: D 281 GLU cc_start: 0.9022 (mp0) cc_final: 0.8670 (mp0) REVERT: D 466 TRP cc_start: 0.6839 (p90) cc_final: 0.6434 (p90) REVERT: D 649 MET cc_start: 0.8218 (tpt) cc_final: 0.7966 (tpp) REVERT: D 659 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.8219 (mtt-85) REVERT: E 515 MET cc_start: 0.8993 (tpp) cc_final: 0.8403 (tpp) REVERT: E 553 LYS cc_start: 0.9331 (mttp) cc_final: 0.8629 (mtmt) REVERT: E 628 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8589 (mm-30) REVERT: E 777 MET cc_start: 0.7363 (mmp) cc_final: 0.6759 (mmt) REVERT: F 303 GLU cc_start: 0.6453 (mp0) cc_final: 0.5875 (mp0) REVERT: F 371 MET cc_start: 0.7360 (tmm) cc_final: 0.6954 (tmm) REVERT: F 603 MET cc_start: 0.8124 (tpp) cc_final: 0.7739 (tpp) REVERT: F 745 GLN cc_start: 0.8730 (mt0) cc_final: 0.8266 (mt0) outliers start: 2 outliers final: 1 residues processed: 403 average time/residue: 0.1588 time to fit residues: 105.1632 Evaluate side-chains 302 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 341 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 301 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 HIS B 426 ASN C 412 GLN C 426 ASN C 738 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.077844 restraints weight = 69829.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.079905 restraints weight = 42814.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081305 restraints weight = 29984.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.082199 restraints weight = 23204.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.082916 restraints weight = 19414.894| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27244 Z= 0.149 Angle : 0.569 9.319 36900 Z= 0.290 Chirality : 0.042 0.157 4196 Planarity : 0.005 0.076 4790 Dihedral : 4.675 59.437 3776 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.77 % Favored : 93.99 % Rotamer: Outliers : 0.07 % Allowed : 2.64 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3397 helix: 1.34 (0.12), residues: 1809 sheet: -0.28 (0.27), residues: 361 loop : -0.77 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 361 TYR 0.035 0.001 TYR D 752 PHE 0.017 0.002 PHE D 587 TRP 0.010 0.001 TRP E 780 HIS 0.003 0.001 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (27242) covalent geometry : angle 0.56862 / 0.29 (36900) hydrogen bonds : bond 0.03564 / 2.43 ( 1308) hydrogen bonds : angle 4.39389 / 3.22 ( 3753) Misc. bond : bond 0.00089 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 400 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 LYS cc_start: 0.8747 (mmtp) cc_final: 0.8524 (ptpt) REVERT: A 546 CYS cc_start: 0.8772 (m) cc_final: 0.8419 (m) REVERT: B 303 GLU cc_start: 0.8285 (mp0) cc_final: 0.8050 (mp0) REVERT: B 305 ASP cc_start: 0.8895 (p0) cc_final: 0.8676 (p0) REVERT: B 327 MET cc_start: 0.8637 (tpp) cc_final: 0.8419 (tpt) REVERT: B 390 LEU cc_start: 0.9099 (tp) cc_final: 0.8895 (tt) REVERT: B 395 ASN cc_start: 0.9151 (t0) cc_final: 0.8911 (t0) REVERT: B 401 LYS cc_start: 0.9142 (mttt) cc_final: 0.8825 (tppt) REVERT: B 546 CYS cc_start: 0.8748 (m) cc_final: 0.8322 (m) REVERT: B 603 MET cc_start: 0.8247 (mmt) cc_final: 0.7892 (mmp) REVERT: B 620 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7775 (ptp-170) REVERT: B 740 MET cc_start: 0.8777 (tmm) cc_final: 0.8408 (tmm) REVERT: B 797 TYR cc_start: 0.7384 (m-80) cc_final: 0.6774 (m-80) REVERT: C 318 MET cc_start: 0.8619 (tmm) cc_final: 0.8238 (tmm) REVERT: C 327 MET cc_start: 0.9239 (tpp) cc_final: 0.8973 (tpp) REVERT: C 369 MET cc_start: 0.8662 (ptm) cc_final: 0.8456 (ptt) REVERT: C 473 MET cc_start: 0.7575 (tpt) cc_final: 0.7192 (tpp) REVERT: C 493 SER cc_start: 0.9209 (m) cc_final: 0.8853 (p) REVERT: C 574 LYS cc_start: 0.8922 (ptmt) cc_final: 0.8650 (ptmt) REVERT: C 652 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7579 (pt0) REVERT: C 741 GLN cc_start: 0.8306 (tp40) cc_final: 0.7936 (tp40) REVERT: D 281 GLU cc_start: 0.9017 (mp0) cc_final: 0.8627 (mp0) REVERT: D 286 ASP cc_start: 0.7913 (t0) cc_final: 0.7705 (t0) REVERT: D 466 TRP cc_start: 0.6746 (p90) cc_final: 0.6200 (p90) REVERT: D 580 GLU cc_start: 0.8814 (mp0) cc_final: 0.8381 (mp0) REVERT: D 649 MET cc_start: 0.8248 (tpt) cc_final: 0.7979 (tpp) REVERT: D 659 ARG cc_start: 0.8672 (mtt-85) cc_final: 0.8359 (mtt-85) REVERT: D 740 MET cc_start: 0.7735 (tmm) cc_final: 0.7402 (tmm) REVERT: E 515 MET cc_start: 0.9012 (tpp) cc_final: 0.8420 (tpp) REVERT: E 628 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8452 (mm-30) REVERT: E 777 MET cc_start: 0.7355 (mmp) cc_final: 0.6741 (mmt) REVERT: F 303 GLU cc_start: 0.6439 (mp0) cc_final: 0.5883 (mp0) REVERT: F 371 MET cc_start: 0.7470 (tmm) cc_final: 0.7090 (tmm) REVERT: F 603 MET cc_start: 0.8200 (tpp) cc_final: 0.7898 (tpp) REVERT: F 745 GLN cc_start: 0.8655 (mt0) cc_final: 0.8281 (mt0) outliers start: 2 outliers final: 0 residues processed: 402 average time/residue: 0.1566 time to fit residues: 104.1297 Evaluate side-chains 298 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 23 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 304 optimal weight: 0.0070 chunk 115 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 426 ASN C 738 ASN C 741 GLN C 745 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.077772 restraints weight = 70145.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.079817 restraints weight = 43173.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081230 restraints weight = 30291.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.082123 restraints weight = 23340.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082835 restraints weight = 19559.306| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27244 Z= 0.146 Angle : 0.569 9.566 36900 Z= 0.289 Chirality : 0.042 0.158 4196 Planarity : 0.004 0.071 4790 Dihedral : 4.697 62.077 3776 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.30 % Favored : 93.46 % Rotamer: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.15), residues: 3397 helix: 1.38 (0.12), residues: 1815 sheet: -0.28 (0.27), residues: 360 loop : -0.80 (0.19), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 646 TYR 0.036 0.001 TYR D 752 PHE 0.022 0.002 PHE B 220 TRP 0.010 0.001 TRP F 500 HIS 0.003 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (27242) covalent geometry : angle 0.56875 / 0.29 (36900) hydrogen bonds : bond 0.03388 / 2.31 ( 1308) hydrogen bonds : angle 4.32573 / 3.17 ( 3753) Misc. bond : bond 0.00089 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 0.934 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: A 546 CYS cc_start: 0.8739 (m) cc_final: 0.8409 (m) REVERT: B 240 LEU cc_start: 0.8633 (tp) cc_final: 0.7963 (tp) REVERT: B 303 GLU cc_start: 0.8322 (mp0) cc_final: 0.7832 (mp0) REVERT: B 305 ASP cc_start: 0.8881 (p0) cc_final: 0.8643 (p0) REVERT: B 390 LEU cc_start: 0.9078 (tp) cc_final: 0.8871 (tt) REVERT: B 395 ASN cc_start: 0.9177 (t0) cc_final: 0.8924 (t0) REVERT: B 401 LYS cc_start: 0.9153 (mttt) cc_final: 0.8796 (tppt) REVERT: B 546 CYS cc_start: 0.8740 (m) cc_final: 0.8289 (m) REVERT: B 603 MET cc_start: 0.8271 (mmt) cc_final: 0.7908 (mmp) REVERT: B 620 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7718 (ptp-170) REVERT: B 740 MET cc_start: 0.8785 (tmm) cc_final: 0.8384 (tmm) REVERT: C 318 MET cc_start: 0.8627 (tmm) cc_final: 0.8218 (tmm) REVERT: C 369 MET cc_start: 0.8638 (ptm) cc_final: 0.8414 (ptt) REVERT: C 473 MET cc_start: 0.7579 (tpt) cc_final: 0.7199 (tpp) REVERT: C 493 SER cc_start: 0.9180 (m) cc_final: 0.8810 (p) REVERT: C 525 GLU cc_start: 0.8047 (pm20) cc_final: 0.7217 (mt-10) REVERT: C 741 GLN cc_start: 0.8284 (tp-100) cc_final: 0.7981 (tp40) REVERT: D 281 GLU cc_start: 0.9019 (mp0) cc_final: 0.8568 (mp0) REVERT: D 286 ASP cc_start: 0.7878 (t0) cc_final: 0.7655 (t0) REVERT: D 466 TRP cc_start: 0.6752 (p90) cc_final: 0.6062 (p90) REVERT: D 580 GLU cc_start: 0.8858 (mp0) cc_final: 0.8330 (mp0) REVERT: D 649 MET cc_start: 0.8241 (tpt) cc_final: 0.7987 (tpp) REVERT: D 659 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8459 (mtt-85) REVERT: D 740 MET cc_start: 0.7719 (tmm) cc_final: 0.7507 (tmm) REVERT: E 515 MET cc_start: 0.8978 (tpp) cc_final: 0.8445 (tpp) REVERT: E 628 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8400 (mm-30) REVERT: E 777 MET cc_start: 0.7371 (mmp) cc_final: 0.6765 (mmt) REVERT: F 219 TRP cc_start: 0.5924 (t-100) cc_final: 0.5690 (t-100) REVERT: F 303 GLU cc_start: 0.6356 (mp0) cc_final: 0.5794 (mp0) REVERT: F 371 MET cc_start: 0.7479 (tmm) cc_final: 0.7157 (tmm) REVERT: F 585 GLN cc_start: 0.8691 (tt0) cc_final: 0.8485 (tp40) REVERT: F 603 MET cc_start: 0.8245 (tpp) cc_final: 0.7873 (tpp) outliers start: 1 outliers final: 0 residues processed: 398 average time/residue: 0.1490 time to fit residues: 98.0331 Evaluate side-chains 298 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 228 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 333 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 156 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 262 optimal weight: 0.0050 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 328 ASN C 412 GLN C 426 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.080087 restraints weight = 69192.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.082216 restraints weight = 42137.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083605 restraints weight = 29286.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.084670 restraints weight = 22626.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.085339 restraints weight = 18686.539| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27244 Z= 0.103 Angle : 0.548 12.788 36900 Z= 0.275 Chirality : 0.041 0.215 4196 Planarity : 0.004 0.081 4790 Dihedral : 4.581 60.019 3776 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.39 % Favored : 94.38 % Rotamer: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3397 helix: 1.50 (0.12), residues: 1812 sheet: -0.26 (0.27), residues: 370 loop : -0.66 (0.20), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 361 TYR 0.034 0.001 TYR D 752 PHE 0.015 0.001 PHE A 476 TRP 0.013 0.001 TRP E 453 HIS 0.003 0.000 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (27242) covalent geometry : angle 0.54766 / 0.27 (36900) hydrogen bonds : bond 0.03028 / 2.07 ( 1308) hydrogen bonds : angle 4.13905 / 3.04 ( 3753) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 0.932 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: A 318 MET cc_start: 0.5279 (tpt) cc_final: 0.4857 (tpp) REVERT: A 406 TYR cc_start: 0.8749 (m-80) cc_final: 0.8532 (m-80) REVERT: A 410 ASP cc_start: 0.8989 (m-30) cc_final: 0.8746 (m-30) REVERT: A 546 CYS cc_start: 0.8723 (m) cc_final: 0.8321 (m) REVERT: A 593 SER cc_start: 0.9153 (m) cc_final: 0.8788 (p) REVERT: A 603 MET cc_start: 0.8755 (mmm) cc_final: 0.8315 (mmp) REVERT: A 772 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7437 (mp0) REVERT: B 240 LEU cc_start: 0.8519 (tp) cc_final: 0.7998 (tp) REVERT: B 303 GLU cc_start: 0.8326 (mp0) cc_final: 0.8013 (mp0) REVERT: B 305 ASP cc_start: 0.8818 (p0) cc_final: 0.8538 (p0) REVERT: B 319 GLU cc_start: 0.7956 (pm20) cc_final: 0.7743 (pm20) REVERT: B 401 LYS cc_start: 0.9134 (mttt) cc_final: 0.8772 (tppt) REVERT: B 546 CYS cc_start: 0.8638 (m) cc_final: 0.8150 (m) REVERT: B 740 MET cc_start: 0.8762 (tmm) cc_final: 0.8304 (tmm) REVERT: B 797 TYR cc_start: 0.7339 (m-80) cc_final: 0.6357 (m-80) REVERT: C 318 MET cc_start: 0.8530 (tmm) cc_final: 0.8113 (tmm) REVERT: C 369 MET cc_start: 0.8636 (ptm) cc_final: 0.8431 (ptt) REVERT: C 493 SER cc_start: 0.9109 (m) cc_final: 0.8779 (p) REVERT: C 525 GLU cc_start: 0.7947 (pm20) cc_final: 0.7221 (mt-10) REVERT: D 272 VAL cc_start: 0.9378 (m) cc_final: 0.9126 (p) REVERT: D 281 GLU cc_start: 0.8933 (mp0) cc_final: 0.8720 (mp0) REVERT: D 286 ASP cc_start: 0.7694 (t0) cc_final: 0.7489 (t0) REVERT: D 466 TRP cc_start: 0.6406 (p90) cc_final: 0.5925 (p90) REVERT: D 473 MET cc_start: 0.8342 (mmm) cc_final: 0.8005 (mmm) REVERT: D 580 GLU cc_start: 0.8818 (mp0) cc_final: 0.8339 (mp0) REVERT: D 649 MET cc_start: 0.8176 (tpt) cc_final: 0.7907 (tpp) REVERT: D 659 ARG cc_start: 0.8684 (mtt-85) cc_final: 0.8475 (mtt-85) REVERT: D 740 MET cc_start: 0.7824 (tmm) cc_final: 0.7606 (tmm) REVERT: E 299 ILE cc_start: 0.9100 (mm) cc_final: 0.8866 (pt) REVERT: E 515 MET cc_start: 0.9026 (tpp) cc_final: 0.8536 (tpp) REVERT: E 628 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8319 (mm-30) REVERT: E 777 MET cc_start: 0.7356 (mmp) cc_final: 0.6775 (mmt) REVERT: F 217 GLU cc_start: 0.7418 (mp0) cc_final: 0.7204 (mp0) REVERT: F 219 TRP cc_start: 0.6049 (t-100) cc_final: 0.5633 (t-100) REVERT: F 303 GLU cc_start: 0.6314 (mp0) cc_final: 0.5755 (mp0) REVERT: F 371 MET cc_start: 0.7409 (tmm) cc_final: 0.7144 (tmm) REVERT: F 539 LEU cc_start: 0.9339 (tp) cc_final: 0.8897 (mp) REVERT: F 603 MET cc_start: 0.8185 (tpp) cc_final: 0.7767 (tpp) REVERT: F 649 MET cc_start: 0.8082 (mpp) cc_final: 0.7820 (mpp) outliers start: 1 outliers final: 0 residues processed: 413 average time/residue: 0.1557 time to fit residues: 105.7921 Evaluate side-chains 306 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 55 optimal weight: 0.9980 chunk 277 optimal weight: 4.9990 chunk 327 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 57 optimal weight: 0.0050 chunk 245 optimal weight: 5.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 328 ASN C 426 ASN ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079700 restraints weight = 69341.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.081730 restraints weight = 42760.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.083176 restraints weight = 30124.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084097 restraints weight = 23211.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084810 restraints weight = 19393.947| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27244 Z= 0.121 Angle : 0.559 10.648 36900 Z= 0.282 Chirality : 0.041 0.182 4196 Planarity : 0.004 0.072 4790 Dihedral : 4.565 60.961 3776 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.06 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 3397 helix: 1.52 (0.12), residues: 1814 sheet: -0.26 (0.27), residues: 370 loop : -0.67 (0.20), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 351 TYR 0.036 0.001 TYR D 752 PHE 0.024 0.002 PHE D 354 TRP 0.011 0.001 TRP E 453 HIS 0.007 0.001 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (27242) covalent geometry : angle 0.55887 / 0.28 (36900) hydrogen bonds : bond 0.03050 / 2.08 ( 1308) hydrogen bonds : angle 4.15238 / 3.04 ( 3753) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 CYS cc_start: 0.8635 (m) cc_final: 0.8249 (m) REVERT: A 603 MET cc_start: 0.8812 (mmm) cc_final: 0.8443 (mmp) REVERT: A 772 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7420 (mm-30) REVERT: B 240 LEU cc_start: 0.8494 (tp) cc_final: 0.7957 (tp) REVERT: B 305 ASP cc_start: 0.8845 (p0) cc_final: 0.8555 (p0) REVERT: B 319 GLU cc_start: 0.8005 (pm20) cc_final: 0.7804 (pm20) REVERT: B 401 LYS cc_start: 0.9165 (mttt) cc_final: 0.8795 (tppt) REVERT: B 546 CYS cc_start: 0.8654 (m) cc_final: 0.8161 (m) REVERT: B 603 MET cc_start: 0.8258 (mmt) cc_final: 0.7833 (mmp) REVERT: B 740 MET cc_start: 0.8756 (tmm) cc_final: 0.8322 (tmm) REVERT: C 318 MET cc_start: 0.8504 (tmm) cc_final: 0.8034 (tmm) REVERT: C 369 MET cc_start: 0.8601 (ptm) cc_final: 0.8366 (ptt) REVERT: C 493 SER cc_start: 0.9181 (m) cc_final: 0.8818 (p) REVERT: C 525 GLU cc_start: 0.8038 (pm20) cc_final: 0.7297 (mt-10) REVERT: C 574 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8670 (ptmt) REVERT: D 272 VAL cc_start: 0.9395 (m) cc_final: 0.9078 (p) REVERT: D 281 GLU cc_start: 0.8980 (mp0) cc_final: 0.8739 (mp0) REVERT: D 466 TRP cc_start: 0.6505 (p90) cc_final: 0.5950 (p90) REVERT: D 580 GLU cc_start: 0.8813 (mp0) cc_final: 0.8312 (mp0) REVERT: D 649 MET cc_start: 0.8179 (tpt) cc_final: 0.7919 (tpp) REVERT: D 659 ARG cc_start: 0.8755 (mtt-85) cc_final: 0.8552 (mtt-85) REVERT: D 740 MET cc_start: 0.7806 (tmm) cc_final: 0.7572 (tmm) REVERT: E 515 MET cc_start: 0.9056 (tpp) cc_final: 0.8517 (tpp) REVERT: E 628 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8343 (mm-30) REVERT: E 777 MET cc_start: 0.7388 (mmp) cc_final: 0.6709 (mmt) REVERT: F 219 TRP cc_start: 0.5867 (t-100) cc_final: 0.5564 (t-100) REVERT: F 303 GLU cc_start: 0.6297 (mp0) cc_final: 0.5747 (mp0) REVERT: F 369 MET cc_start: 0.3072 (mpp) cc_final: 0.2773 (mpp) REVERT: F 371 MET cc_start: 0.7491 (tmm) cc_final: 0.7186 (tmm) REVERT: F 603 MET cc_start: 0.8166 (tpp) cc_final: 0.7739 (tpp) REVERT: F 649 MET cc_start: 0.8112 (mpp) cc_final: 0.7873 (mpp) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.1500 time to fit residues: 99.4230 Evaluate side-chains 301 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 106 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 459 HIS C 328 ASN C 426 ASN C 738 ASN ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS F 484 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.077638 restraints weight = 70438.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.079680 restraints weight = 43834.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081061 restraints weight = 30773.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081943 restraints weight = 23885.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082647 restraints weight = 20008.811| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27244 Z= 0.176 Angle : 0.617 10.530 36900 Z= 0.312 Chirality : 0.043 0.198 4196 Planarity : 0.005 0.095 4790 Dihedral : 4.753 65.629 3776 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.59 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 3397 helix: 1.42 (0.12), residues: 1820 sheet: -0.27 (0.27), residues: 359 loop : -0.74 (0.20), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 332 TYR 0.034 0.002 TYR D 752 PHE 0.023 0.002 PHE E 476 TRP 0.031 0.001 TRP C 219 HIS 0.009 0.001 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (27242) covalent geometry : angle 0.61674 / 0.31 (36900) hydrogen bonds : bond 0.03320 / 2.28 ( 1308) hydrogen bonds : angle 4.31312 / 3.15 ( 3753) Misc. bond : bond 0.00085 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8856 (tp30) REVERT: A 240 LEU cc_start: 0.9188 (tp) cc_final: 0.8954 (tp) REVERT: A 318 MET cc_start: 0.5420 (tpt) cc_final: 0.4929 (tpp) REVERT: A 515 MET cc_start: 0.8510 (ttm) cc_final: 0.7837 (tmm) REVERT: A 546 CYS cc_start: 0.8682 (m) cc_final: 0.8302 (m) REVERT: A 566 ILE cc_start: 0.9683 (mm) cc_final: 0.9481 (mm) REVERT: A 603 MET cc_start: 0.8856 (mmm) cc_final: 0.8475 (mmp) REVERT: B 240 LEU cc_start: 0.8591 (tp) cc_final: 0.8009 (tp) REVERT: B 305 ASP cc_start: 0.8913 (p0) cc_final: 0.8633 (p0) REVERT: B 401 LYS cc_start: 0.9122 (mttt) cc_final: 0.8792 (tppt) REVERT: B 546 CYS cc_start: 0.8780 (m) cc_final: 0.8306 (m) REVERT: B 603 MET cc_start: 0.8192 (mmt) cc_final: 0.7866 (mmp) REVERT: B 740 MET cc_start: 0.8803 (tmm) cc_final: 0.8562 (tmm) REVERT: C 318 MET cc_start: 0.8581 (tmm) cc_final: 0.8097 (tmm) REVERT: C 369 MET cc_start: 0.8616 (ptm) cc_final: 0.8400 (ptt) REVERT: C 493 SER cc_start: 0.9207 (m) cc_final: 0.8894 (p) REVERT: C 571 LEU cc_start: 0.8703 (mt) cc_final: 0.8495 (mt) REVERT: C 574 LYS cc_start: 0.8949 (ptmt) cc_final: 0.8674 (ptmt) REVERT: C 603 MET cc_start: 0.8731 (mmp) cc_final: 0.8107 (mmp) REVERT: C 741 GLN cc_start: 0.8501 (tp40) cc_final: 0.8258 (tp-100) REVERT: D 231 MET cc_start: 0.6172 (mmm) cc_final: 0.5818 (tpt) REVERT: D 272 VAL cc_start: 0.9452 (m) cc_final: 0.9087 (p) REVERT: D 398 GLU cc_start: 0.8592 (tp30) cc_final: 0.7903 (tp30) REVERT: D 402 MET cc_start: 0.8867 (mtm) cc_final: 0.8246 (mpp) REVERT: D 466 TRP cc_start: 0.6743 (p90) cc_final: 0.5923 (p90) REVERT: D 580 GLU cc_start: 0.8799 (mp0) cc_final: 0.8214 (mp0) REVERT: D 649 MET cc_start: 0.8248 (tpt) cc_final: 0.7987 (tpp) REVERT: D 659 ARG cc_start: 0.8761 (mtt-85) cc_final: 0.8555 (mtt-85) REVERT: D 740 MET cc_start: 0.7810 (tmm) cc_final: 0.7541 (tmm) REVERT: E 515 MET cc_start: 0.9027 (tpp) cc_final: 0.8481 (tpp) REVERT: E 628 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8439 (mm-30) REVERT: E 777 MET cc_start: 0.7319 (mmp) cc_final: 0.6699 (mmt) REVERT: F 303 GLU cc_start: 0.6443 (mp0) cc_final: 0.5867 (mp0) REVERT: F 367 ILE cc_start: 0.7165 (mt) cc_final: 0.6917 (mt) REVERT: F 369 MET cc_start: 0.2862 (mpp) cc_final: 0.2574 (mpp) REVERT: F 371 MET cc_start: 0.7523 (tmm) cc_final: 0.7258 (tmm) REVERT: F 603 MET cc_start: 0.8137 (tpp) cc_final: 0.7694 (tpp) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1581 time to fit residues: 103.0598 Evaluate side-chains 298 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 250 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 287 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 301 optimal weight: 0.3980 chunk 149 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 328 ASN C 426 ASN C 645 ASN C 738 ASN ** C 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 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 = 0.3421 r_free = 0.3421 target = 0.101419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.080141 restraints weight = 69452.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.082311 restraints weight = 42062.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083784 restraints weight = 29146.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.084787 restraints weight = 22282.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085485 restraints weight = 18371.315| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27244 Z= 0.106 Angle : 0.577 12.008 36900 Z= 0.288 Chirality : 0.042 0.187 4196 Planarity : 0.005 0.070 4790 Dihedral : 4.622 63.319 3776 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.53 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3397 helix: 1.47 (0.12), residues: 1826 sheet: -0.24 (0.27), residues: 367 loop : -0.70 (0.20), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 332 TYR 0.035 0.001 TYR D 752 PHE 0.025 0.002 PHE B 220 TRP 0.023 0.001 TRP C 219 HIS 0.006 0.001 HIS B 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (27242) covalent geometry : angle 0.57721 / 0.29 (36900) hydrogen bonds : bond 0.02987 / 2.02 ( 1308) hydrogen bonds : angle 4.12786 / 3.03 ( 3753) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8778 (tp30) REVERT: A 318 MET cc_start: 0.5470 (tpt) cc_final: 0.5013 (tpp) REVERT: A 546 CYS cc_start: 0.8573 (m) cc_final: 0.8117 (m) REVERT: A 603 MET cc_start: 0.8832 (mmm) cc_final: 0.8577 (mmp) REVERT: B 240 LEU cc_start: 0.8564 (tp) cc_final: 0.7939 (tp) REVERT: B 305 ASP cc_start: 0.8840 (p0) cc_final: 0.8527 (p0) REVERT: B 319 GLU cc_start: 0.7923 (pm20) cc_final: 0.7678 (pm20) REVERT: B 401 LYS cc_start: 0.9134 (mttt) cc_final: 0.8770 (tppt) REVERT: B 546 CYS cc_start: 0.8685 (m) cc_final: 0.8100 (m) REVERT: B 654 ILE cc_start: 0.9326 (mt) cc_final: 0.9118 (tt) REVERT: B 740 MET cc_start: 0.8765 (tmm) cc_final: 0.8365 (tmm) REVERT: C 318 MET cc_start: 0.8515 (tmm) cc_final: 0.8310 (tpt) REVERT: C 369 MET cc_start: 0.8596 (ptm) cc_final: 0.8356 (ptt) REVERT: C 493 SER cc_start: 0.9141 (m) cc_final: 0.8809 (p) REVERT: C 525 GLU cc_start: 0.8141 (pm20) cc_final: 0.7464 (mt-10) REVERT: C 574 LYS cc_start: 0.8899 (ptmt) cc_final: 0.8633 (ptmt) REVERT: D 231 MET cc_start: 0.6184 (mmm) cc_final: 0.5981 (tpt) REVERT: D 272 VAL cc_start: 0.9387 (m) cc_final: 0.9040 (p) REVERT: D 398 GLU cc_start: 0.8436 (tp30) cc_final: 0.7611 (tp30) REVERT: D 402 MET cc_start: 0.8822 (mtm) cc_final: 0.8130 (mpp) REVERT: D 466 TRP cc_start: 0.6378 (p90) cc_final: 0.5890 (p90) REVERT: D 580 GLU cc_start: 0.8808 (mp0) cc_final: 0.8328 (mp0) REVERT: D 649 MET cc_start: 0.8136 (tpt) cc_final: 0.7899 (tpp) REVERT: D 659 ARG cc_start: 0.8698 (mtt-85) cc_final: 0.8469 (mtt-85) REVERT: E 299 ILE cc_start: 0.9198 (mm) cc_final: 0.8837 (pt) REVERT: E 515 MET cc_start: 0.9020 (tpp) cc_final: 0.8555 (tpp) REVERT: E 628 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 777 MET cc_start: 0.7315 (mmp) cc_final: 0.6677 (mmt) REVERT: F 219 TRP cc_start: 0.5969 (t-100) cc_final: 0.5606 (t-100) REVERT: F 303 GLU cc_start: 0.6361 (mp0) cc_final: 0.5828 (mp0) REVERT: F 367 ILE cc_start: 0.7236 (mt) cc_final: 0.6963 (mt) REVERT: F 369 MET cc_start: 0.2755 (mpp) cc_final: 0.2496 (mpp) REVERT: F 371 MET cc_start: 0.7522 (tmm) cc_final: 0.7286 (tmm) REVERT: F 539 LEU cc_start: 0.9351 (tp) cc_final: 0.8930 (mp) REVERT: F 603 MET cc_start: 0.8164 (tpp) cc_final: 0.7940 (tpp) REVERT: F 649 MET cc_start: 0.8136 (mpp) cc_final: 0.7904 (mpp) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.1571 time to fit residues: 106.8312 Evaluate side-chains 311 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 45 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 217 optimal weight: 0.0070 chunk 195 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 328 ASN C 426 ASN C 738 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.100108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079240 restraints weight = 69765.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081257 restraints weight = 43204.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082605 restraints weight = 30443.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.083608 restraints weight = 23608.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084230 restraints weight = 19576.771| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27244 Z= 0.135 Angle : 0.587 11.745 36900 Z= 0.294 Chirality : 0.042 0.181 4196 Planarity : 0.005 0.103 4790 Dihedral : 4.611 64.641 3776 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.36 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3397 helix: 1.49 (0.12), residues: 1822 sheet: -0.25 (0.27), residues: 370 loop : -0.67 (0.20), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 332 TYR 0.034 0.001 TYR D 752 PHE 0.018 0.002 PHE F 423 TRP 0.017 0.001 TRP C 219 HIS 0.005 0.001 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (27242) covalent geometry : angle 0.58740 / 0.29 (36900) hydrogen bonds : bond 0.03044 / 2.09 ( 1308) hydrogen bonds : angle 4.16217 / 3.04 ( 3753) Misc. bond : bond 0.00038 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8821 (tp30) REVERT: A 318 MET cc_start: 0.5489 (tpt) cc_final: 0.5010 (tpp) REVERT: A 546 CYS cc_start: 0.8589 (m) cc_final: 0.8208 (m) REVERT: A 603 MET cc_start: 0.8861 (mmm) cc_final: 0.8467 (mmp) REVERT: A 772 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7308 (mm-30) REVERT: B 240 LEU cc_start: 0.8581 (tp) cc_final: 0.7968 (tp) REVERT: B 305 ASP cc_start: 0.8910 (p0) cc_final: 0.8623 (p0) REVERT: B 401 LYS cc_start: 0.9132 (mttt) cc_final: 0.8783 (tppt) REVERT: B 546 CYS cc_start: 0.8705 (m) cc_final: 0.8196 (m) REVERT: B 740 MET cc_start: 0.8770 (tmm) cc_final: 0.8344 (tmm) REVERT: C 318 MET cc_start: 0.8571 (tmm) cc_final: 0.8199 (tpt) REVERT: C 368 ASP cc_start: 0.8788 (t70) cc_final: 0.8447 (t0) REVERT: C 369 MET cc_start: 0.8579 (ptm) cc_final: 0.8226 (ptt) REVERT: C 493 SER cc_start: 0.9120 (m) cc_final: 0.8806 (p) REVERT: C 525 GLU cc_start: 0.8089 (pm20) cc_final: 0.7249 (mt-10) REVERT: C 574 LYS cc_start: 0.8914 (ptmt) cc_final: 0.8664 (ptmt) REVERT: D 231 MET cc_start: 0.6129 (mmm) cc_final: 0.5739 (tpt) REVERT: D 272 VAL cc_start: 0.9408 (m) cc_final: 0.9029 (p) REVERT: D 286 ASP cc_start: 0.7807 (t70) cc_final: 0.7600 (t0) REVERT: D 398 GLU cc_start: 0.8428 (tp30) cc_final: 0.7584 (tp30) REVERT: D 402 MET cc_start: 0.8831 (mtm) cc_final: 0.8073 (mpp) REVERT: D 466 TRP cc_start: 0.6570 (p90) cc_final: 0.5920 (p90) REVERT: D 580 GLU cc_start: 0.8715 (mp0) cc_final: 0.8294 (mp0) REVERT: D 649 MET cc_start: 0.8191 (tpt) cc_final: 0.7952 (tpp) REVERT: D 659 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.8461 (mtt-85) REVERT: E 515 MET cc_start: 0.9020 (tpp) cc_final: 0.8548 (tpp) REVERT: E 628 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 777 MET cc_start: 0.7271 (mmp) cc_final: 0.6592 (mmt) REVERT: F 219 TRP cc_start: 0.5937 (t-100) cc_final: 0.5634 (t-100) REVERT: F 303 GLU cc_start: 0.6365 (mp0) cc_final: 0.5838 (mp0) REVERT: F 367 ILE cc_start: 0.7194 (mt) cc_final: 0.6943 (mt) REVERT: F 369 MET cc_start: 0.2756 (mpp) cc_final: 0.2527 (mpp) REVERT: F 371 MET cc_start: 0.7539 (tmm) cc_final: 0.7260 (tmm) REVERT: F 539 LEU cc_start: 0.9348 (tp) cc_final: 0.8927 (mp) REVERT: F 603 MET cc_start: 0.8154 (tpp) cc_final: 0.7937 (tpp) REVERT: F 649 MET cc_start: 0.8221 (mpp) cc_final: 0.7974 (mpp) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1511 time to fit residues: 100.9585 Evaluate side-chains 306 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 84 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 328 ASN C 426 ASN C 645 ASN C 738 ASN C 745 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.077828 restraints weight = 69609.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.079813 restraints weight = 43198.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081181 restraints weight = 30389.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081970 restraints weight = 23462.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.082711 restraints weight = 19819.953| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27244 Z= 0.176 Angle : 0.620 11.341 36900 Z= 0.312 Chirality : 0.042 0.189 4196 Planarity : 0.005 0.106 4790 Dihedral : 4.736 66.518 3776 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.71 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 3397 helix: 1.46 (0.12), residues: 1824 sheet: -0.14 (0.27), residues: 353 loop : -0.75 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 332 TYR 0.016 0.001 TYR A 752 PHE 0.025 0.002 PHE B 220 TRP 0.017 0.001 TRP C 219 HIS 0.007 0.001 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (27242) covalent geometry : angle 0.62034 / 0.31 (36900) hydrogen bonds : bond 0.03221 / 2.20 ( 1308) hydrogen bonds : angle 4.27396 / 3.12 ( 3753) Misc. bond : bond 0.00091 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3789.64 seconds wall clock time: 82 minutes 32.70 seconds (4952.70 seconds total)