Starting phenix.real_space_refine on Fri Mar 6 00:51:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3i_25659/03_2026/7t3i_25659.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3i_25659/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3i_25659/03_2026/7t3i_25659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3i_25659/03_2026/7t3i_25659.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3i_25659/03_2026/7t3i_25659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3i_25659/03_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-5986/lib/python3.9/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: 6.29, per 1000 atoms: 0.23 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: 1.97 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: 0.90 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: 4.92 Time building geometry restraints manager: 2.73 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: 15429 18.01 - 36.02: 1238 36.02 - 54.03: 171 54.03 - 72.04: 80 72.04 - 90.05: 24 Dihedral angle restraints: 16942 sinusoidal: 7009 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 16939 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 24.090 Find NCS groups from input model: 0.670 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 13.812 90.047 10510 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 covalent geometry : bond 0.00257 (27242) covalent geometry : angle 0.58666 (36900) hydrogen bonds : bond 0.18431 ( 1308) hydrogen bonds : angle 5.90610 ( 3753) Misc. bond : bond 0.00052 ( 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 : 1.013 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: 0.1614 time to fit residues: 118.5423 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 : 1.033 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.100579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.079817 restraints weight = 69560.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.081959 restraints weight = 42556.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.083389 restraints weight = 29470.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084402 restraints weight = 22602.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085016 restraints weight = 18644.055| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27244 Z= 0.121 Angle : 0.560 8.680 36900 Z= 0.288 Chirality : 0.042 0.220 4196 Planarity : 0.005 0.054 4790 Dihedral : 10.069 88.033 4024 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.27 % Favored : 94.50 % Rotamer: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.88 % 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: 0.62 (0.15), residues: 3397 helix: 1.33 (0.12), residues: 1787 sheet: -0.15 (0.27), residues: 364 loop : -0.69 (0.19), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.024 0.001 TYR D 413 PHE 0.015 0.002 PHE C 731 TRP 0.025 0.002 TRP B 219 HIS 0.005 0.001 HIS E 438 Details of bonding type rmsd covalent geometry : bond 0.00265 (27242) covalent geometry : angle 0.55986 (36900) hydrogen bonds : bond 0.04001 ( 1308) hydrogen bonds : angle 4.54719 ( 3753) Misc. bond : bond 0.00025 ( 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 427 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 424 time to evaluate : 0.948 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 286 ASP cc_start: 0.8638 (m-30) cc_final: 0.7980 (p0) REVERT: A 522 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8478 (ptmt) REVERT: A 539 LEU cc_start: 0.9483 (tp) cc_final: 0.9256 (tt) REVERT: A 546 CYS cc_start: 0.8783 (m) cc_final: 0.8422 (m) REVERT: B 240 LEU cc_start: 0.8480 (tp) cc_final: 0.7853 (tp) REVERT: B 320 SER cc_start: 0.9254 (t) cc_final: 0.8852 (m) REVERT: B 327 MET cc_start: 0.8571 (tpp) cc_final: 0.8172 (tpt) REVERT: B 395 ASN cc_start: 0.9169 (t0) cc_final: 0.8894 (t0) REVERT: B 401 LYS cc_start: 0.9158 (mttt) cc_final: 0.8846 (tppt) REVERT: B 546 CYS cc_start: 0.8645 (m) cc_final: 0.8140 (m) REVERT: B 740 MET cc_start: 0.8632 (tmm) cc_final: 0.8344 (tmm) REVERT: C 318 MET cc_start: 0.8615 (tmm) cc_final: 0.8294 (tmm) REVERT: C 368 ASP cc_start: 0.8763 (t70) cc_final: 0.8359 (t0) REVERT: C 493 SER cc_start: 0.9174 (m) cc_final: 0.8843 (p) REVERT: C 574 LYS cc_start: 0.8897 (ptmt) cc_final: 0.8606 (ptmt) REVERT: C 652 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7496 (mt-10) REVERT: C 741 GLN cc_start: 0.8369 (tp40) cc_final: 0.8080 (tp40) REVERT: D 204 ILE cc_start: 0.9122 (tt) cc_final: 0.8902 (pt) REVERT: D 286 ASP cc_start: 0.7817 (t70) cc_final: 0.7585 (t0) REVERT: D 416 LYS cc_start: 0.9042 (tppt) cc_final: 0.8015 (tppt) REVERT: D 466 TRP cc_start: 0.6486 (p90) cc_final: 0.6239 (p90) REVERT: D 473 MET cc_start: 0.8240 (mmm) cc_final: 0.8027 (mmm) REVERT: D 580 GLU cc_start: 0.8846 (mp0) cc_final: 0.8462 (mp0) REVERT: D 649 MET cc_start: 0.8154 (tpt) cc_final: 0.7861 (tpp) REVERT: D 659 ARG cc_start: 0.8690 (mtt90) cc_final: 0.8385 (mtt-85) REVERT: D 740 MET cc_start: 0.7949 (tmm) cc_final: 0.7576 (tmm) REVERT: E 235 TYR cc_start: 0.7354 (t80) cc_final: 0.6395 (t80) REVERT: E 515 MET cc_start: 0.8881 (tpp) cc_final: 0.8308 (tpp) REVERT: E 624 THR cc_start: 0.9548 (p) cc_final: 0.9148 (t) REVERT: F 303 GLU cc_start: 0.6460 (mp0) cc_final: 0.5945 (mp0) REVERT: F 371 MET cc_start: 0.7222 (tmm) cc_final: 0.6452 (mmt) REVERT: F 482 LEU cc_start: 0.9043 (mt) cc_final: 0.8822 (tt) REVERT: F 539 LEU cc_start: 0.9417 (tp) cc_final: 0.9066 (mp) REVERT: F 745 GLN cc_start: 0.8719 (mt0) cc_final: 0.8384 (pt0) outliers start: 3 outliers final: 0 residues processed: 426 average time/residue: 0.1633 time to fit residues: 113.0388 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 : 1.112 ------------------------------------------------------------------------------- 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: 6.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 0.0870 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 585 GLN B 426 ASN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN C 785 ASN D 442 HIS 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 = 0.3354 r_free = 0.3354 target = 0.097263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.076047 restraints weight = 70985.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.078153 restraints weight = 42944.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.079608 restraints weight = 29781.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.080591 restraints weight = 22803.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081205 restraints weight = 18848.336| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27244 Z= 0.211 Angle : 0.622 7.696 36900 Z= 0.320 Chirality : 0.043 0.201 4196 Planarity : 0.005 0.053 4790 Dihedral : 10.056 89.781 4024 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.74 % Favored : 93.02 % Rotamer: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % 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: 0.49 (0.15), residues: 3397 helix: 1.24 (0.12), residues: 1812 sheet: -0.27 (0.27), residues: 352 loop : -0.79 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 361 TYR 0.033 0.002 TYR D 752 PHE 0.020 0.002 PHE D 587 TRP 0.015 0.002 TRP C 219 HIS 0.007 0.001 HIS E 459 Details of bonding type rmsd covalent geometry : bond 0.00478 (27242) covalent geometry : angle 0.62204 (36900) hydrogen bonds : bond 0.04078 ( 1308) hydrogen bonds : angle 4.59002 ( 3753) Misc. bond : bond 0.00080 ( 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 402 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 399 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.8084 (mmt) cc_final: 0.7815 (mmm) REVERT: A 522 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8512 (ptmt) REVERT: A 546 CYS cc_start: 0.8826 (m) cc_final: 0.8478 (m) REVERT: A 566 ILE cc_start: 0.9622 (mm) cc_final: 0.9410 (mm) REVERT: B 240 LEU cc_start: 0.8575 (tp) cc_final: 0.7978 (tp) REVERT: B 302 ASP cc_start: 0.8313 (p0) cc_final: 0.7272 (p0) REVERT: B 305 ASP cc_start: 0.8963 (p0) cc_final: 0.8724 (p0) REVERT: B 327 MET cc_start: 0.8649 (tpp) cc_final: 0.8432 (tpt) REVERT: B 395 ASN cc_start: 0.9166 (t0) cc_final: 0.8935 (t0) REVERT: B 401 LYS cc_start: 0.9185 (mttt) cc_final: 0.8860 (tppt) REVERT: B 546 CYS cc_start: 0.8762 (m) cc_final: 0.8356 (m) REVERT: B 740 MET cc_start: 0.8770 (tmm) cc_final: 0.8425 (tmm) REVERT: C 231 MET cc_start: 0.7379 (ptp) cc_final: 0.7019 (mtm) REVERT: C 318 MET cc_start: 0.8657 (tmm) cc_final: 0.8315 (tmm) REVERT: C 327 MET cc_start: 0.9231 (tpp) cc_final: 0.9022 (tpp) REVERT: C 369 MET cc_start: 0.8678 (ptm) cc_final: 0.8417 (ptt) REVERT: C 473 MET cc_start: 0.7487 (tpt) cc_final: 0.7254 (tpp) REVERT: C 525 GLU cc_start: 0.8125 (pm20) cc_final: 0.7353 (mt-10) REVERT: C 574 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8650 (ptmt) REVERT: C 596 CYS cc_start: 0.8753 (t) cc_final: 0.8330 (p) REVERT: C 741 GLN cc_start: 0.8318 (tp40) cc_final: 0.7864 (tp-100) REVERT: D 204 ILE cc_start: 0.9152 (tt) cc_final: 0.8938 (pt) REVERT: D 281 GLU cc_start: 0.9032 (mp0) cc_final: 0.8672 (mp0) REVERT: D 398 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8501 (mm-30) REVERT: D 466 TRP cc_start: 0.6864 (p90) cc_final: 0.6415 (p90) REVERT: D 649 MET cc_start: 0.8232 (tpt) cc_final: 0.7967 (tpp) REVERT: D 659 ARG cc_start: 0.8732 (mtt90) cc_final: 0.8390 (mtt-85) REVERT: D 740 MET cc_start: 0.7973 (tmm) cc_final: 0.7548 (tmm) REVERT: E 515 MET cc_start: 0.9006 (tpp) cc_final: 0.8411 (tpp) REVERT: E 628 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8585 (mm-30) REVERT: E 777 MET cc_start: 0.7509 (mmp) cc_final: 0.6893 (mmt) REVERT: F 219 TRP cc_start: 0.5821 (t-100) cc_final: 0.5607 (t-100) REVERT: F 303 GLU cc_start: 0.6458 (mp0) cc_final: 0.5878 (mp0) REVERT: F 371 MET cc_start: 0.7362 (tmm) cc_final: 0.6952 (tmm) REVERT: F 603 MET cc_start: 0.8088 (tpp) cc_final: 0.7782 (tpp) REVERT: F 745 GLN cc_start: 0.8700 (mt0) cc_final: 0.8291 (mt0) outliers start: 3 outliers final: 1 residues processed: 402 average time/residue: 0.1562 time to fit residues: 103.4201 Evaluate side-chains 298 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 412 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN C 741 GLN C 745 GLN D 585 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS F 484 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.076172 restraints weight = 70193.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078225 restraints weight = 43640.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.079573 restraints weight = 30580.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.080457 restraints weight = 23728.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.081147 restraints weight = 19881.199| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27244 Z= 0.199 Angle : 0.609 8.466 36900 Z= 0.312 Chirality : 0.043 0.182 4196 Planarity : 0.005 0.081 4790 Dihedral : 9.932 83.558 4024 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.56 % Favored : 93.20 % Rotamer: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % 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: 0.43 (0.15), residues: 3397 helix: 1.21 (0.12), residues: 1817 sheet: -0.22 (0.27), residues: 355 loop : -0.90 (0.19), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 361 TYR 0.034 0.002 TYR D 752 PHE 0.020 0.002 PHE D 587 TRP 0.014 0.001 TRP C 219 HIS 0.004 0.001 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00449 (27242) covalent geometry : angle 0.60886 (36900) hydrogen bonds : bond 0.03723 ( 1308) hydrogen bonds : angle 4.52148 ( 3753) Misc. bond : bond 0.00109 ( 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 395 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 0.953 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: 0.8786 (m) cc_final: 0.8460 (m) REVERT: B 240 LEU cc_start: 0.8528 (tp) cc_final: 0.7919 (tp) REVERT: B 303 GLU cc_start: 0.8373 (mp0) cc_final: 0.8056 (mp0) REVERT: B 395 ASN cc_start: 0.9160 (t0) cc_final: 0.8907 (t0) REVERT: B 401 LYS cc_start: 0.9163 (mttt) cc_final: 0.8845 (tppt) REVERT: B 546 CYS cc_start: 0.8776 (m) cc_final: 0.8318 (m) REVERT: B 603 MET cc_start: 0.8296 (mmt) cc_final: 0.7989 (mmp) REVERT: B 620 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7793 (ptp-170) REVERT: B 740 MET cc_start: 0.8820 (tmm) cc_final: 0.8439 (tmm) REVERT: B 797 TYR cc_start: 0.7490 (m-80) cc_final: 0.6909 (m-80) REVERT: C 318 MET cc_start: 0.8643 (tmm) cc_final: 0.8251 (tmm) REVERT: C 327 MET cc_start: 0.9256 (tpp) cc_final: 0.9026 (tpp) REVERT: C 369 MET cc_start: 0.8673 (ptm) cc_final: 0.8460 (ptt) REVERT: C 473 MET cc_start: 0.7538 (tpt) cc_final: 0.7208 (tpp) REVERT: C 493 SER cc_start: 0.9238 (m) cc_final: 0.8933 (p) REVERT: C 574 LYS cc_start: 0.8946 (ptmt) cc_final: 0.8677 (ptmt) REVERT: C 652 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7613 (pt0) REVERT: C 741 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7959 (tp-100) REVERT: D 204 ILE cc_start: 0.9150 (tt) cc_final: 0.8899 (pt) REVERT: D 231 MET cc_start: 0.6513 (mmm) cc_final: 0.6071 (tpt) REVERT: D 286 ASP cc_start: 0.7953 (t0) cc_final: 0.7736 (t0) REVERT: D 466 TRP cc_start: 0.6898 (p90) cc_final: 0.6342 (p90) REVERT: D 649 MET cc_start: 0.8299 (tpt) cc_final: 0.8042 (tpp) REVERT: D 659 ARG cc_start: 0.8764 (mtt90) cc_final: 0.8447 (mtt-85) REVERT: D 740 MET cc_start: 0.8081 (tmm) cc_final: 0.7764 (tmm) REVERT: E 406 TYR cc_start: 0.7737 (m-10) cc_final: 0.7480 (m-10) REVERT: E 515 MET cc_start: 0.8985 (tpp) cc_final: 0.8391 (tpp) REVERT: E 553 LYS cc_start: 0.9365 (mttp) cc_final: 0.8688 (mtmt) REVERT: E 626 LEU cc_start: 0.8884 (mm) cc_final: 0.8408 (mm) REVERT: E 628 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8410 (mm-30) REVERT: E 777 MET cc_start: 0.7379 (mmp) cc_final: 0.6737 (mmt) REVERT: F 219 TRP cc_start: 0.5853 (t-100) cc_final: 0.5627 (t-100) REVERT: F 303 GLU cc_start: 0.6378 (mp0) cc_final: 0.5822 (mp0) REVERT: F 371 MET cc_start: 0.7418 (tmm) cc_final: 0.7020 (tmm) REVERT: F 585 GLN cc_start: 0.8711 (tt0) cc_final: 0.8477 (tp40) REVERT: F 603 MET cc_start: 0.8236 (tpp) cc_final: 0.7862 (tpp) REVERT: F 745 GLN cc_start: 0.8636 (mt0) cc_final: 0.8300 (mt0) outliers start: 2 outliers final: 1 residues processed: 395 average time/residue: 0.1594 time to fit residues: 103.4491 Evaluate side-chains 298 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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: 7.9990 chunk 129 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN E 342 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.077341 restraints weight = 69974.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.079456 restraints weight = 42256.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.080898 restraints weight = 29342.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081860 restraints weight = 22605.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082595 restraints weight = 18787.834| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27244 Z= 0.142 Angle : 0.573 10.634 36900 Z= 0.292 Chirality : 0.042 0.220 4196 Planarity : 0.004 0.068 4790 Dihedral : 9.742 87.219 4024 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.45 % Favored : 93.32 % Rotamer: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.08 % 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: 1.36 (0.12), residues: 1812 sheet: -0.19 (0.27), residues: 351 loop : -0.84 (0.19), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 361 TYR 0.038 0.001 TYR D 752 PHE 0.023 0.002 PHE B 220 TRP 0.015 0.001 TRP E 453 HIS 0.003 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00322 (27242) covalent geometry : angle 0.57327 (36900) hydrogen bonds : bond 0.03373 ( 1308) hydrogen bonds : angle 4.35808 ( 3753) Misc. bond : bond 0.00043 ( 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 394 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.8061 (mmt) cc_final: 0.7829 (mmm) REVERT: A 546 CYS cc_start: 0.8748 (m) cc_final: 0.8436 (m) REVERT: B 240 LEU cc_start: 0.8534 (tp) cc_final: 0.7978 (tp) REVERT: B 401 LYS cc_start: 0.9176 (mttt) cc_final: 0.8833 (tppt) REVERT: B 546 CYS cc_start: 0.8744 (m) cc_final: 0.8242 (m) REVERT: B 603 MET cc_start: 0.8284 (mmt) cc_final: 0.8068 (mmp) REVERT: B 620 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7800 (ptp-170) REVERT: B 740 MET cc_start: 0.8786 (tmm) cc_final: 0.8332 (tmm) REVERT: C 318 MET cc_start: 0.8597 (tmm) cc_final: 0.8174 (tmm) REVERT: C 369 MET cc_start: 0.8652 (ptm) cc_final: 0.8430 (ptt) REVERT: C 473 MET cc_start: 0.7506 (tpt) cc_final: 0.7231 (tpp) REVERT: C 493 SER cc_start: 0.9189 (m) cc_final: 0.8845 (p) REVERT: C 525 GLU cc_start: 0.8041 (pm20) cc_final: 0.7199 (mt-10) REVERT: C 574 LYS cc_start: 0.8931 (ptmt) cc_final: 0.8658 (ptmt) REVERT: C 741 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7867 (tp-100) REVERT: D 286 ASP cc_start: 0.7854 (t0) cc_final: 0.7617 (t0) REVERT: D 402 MET cc_start: 0.8728 (mtm) cc_final: 0.8509 (mtm) REVERT: D 466 TRP cc_start: 0.6824 (p90) cc_final: 0.6003 (p90) REVERT: D 580 GLU cc_start: 0.8826 (mp0) cc_final: 0.8413 (mp0) REVERT: D 649 MET cc_start: 0.8233 (tpt) cc_final: 0.7980 (tpp) REVERT: D 740 MET cc_start: 0.8087 (tmm) cc_final: 0.7752 (tmm) REVERT: E 406 TYR cc_start: 0.7688 (m-10) cc_final: 0.7466 (m-10) REVERT: E 515 MET cc_start: 0.9010 (tpp) cc_final: 0.8467 (tpp) REVERT: E 628 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8402 (mm-30) REVERT: E 777 MET cc_start: 0.7356 (mmp) cc_final: 0.6750 (mmt) REVERT: F 219 TRP cc_start: 0.5902 (t-100) cc_final: 0.5648 (t-100) REVERT: F 303 GLU cc_start: 0.6360 (mp0) cc_final: 0.5782 (mp0) REVERT: F 371 MET cc_start: 0.7479 (tmm) cc_final: 0.7140 (tmm) REVERT: F 585 GLN cc_start: 0.8671 (tt0) cc_final: 0.8463 (tp40) REVERT: F 603 MET cc_start: 0.8218 (tpp) cc_final: 0.7755 (tpp) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.1534 time to fit residues: 101.0269 Evaluate side-chains 296 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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: 4.9990 chunk 173 optimal weight: 2.9990 chunk 333 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 328 ASN C 412 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN E 426 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.077358 restraints weight = 70204.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.079316 restraints weight = 43686.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.080748 restraints weight = 31056.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.081673 restraints weight = 24023.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.082371 restraints weight = 20066.384| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27244 Z= 0.153 Angle : 0.577 10.280 36900 Z= 0.293 Chirality : 0.042 0.165 4196 Planarity : 0.005 0.086 4790 Dihedral : 9.685 86.117 4024 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.61 % Rotamer: Outliers : 0.04 % Allowed : 1.83 % Favored : 98.13 % 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: 0.62 (0.15), residues: 3397 helix: 1.38 (0.12), residues: 1813 sheet: -0.18 (0.27), residues: 351 loop : -0.83 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 361 TYR 0.036 0.001 TYR D 752 PHE 0.015 0.002 PHE A 476 TRP 0.012 0.001 TRP D 453 HIS 0.004 0.001 HIS B 459 Details of bonding type rmsd covalent geometry : bond 0.00348 (27242) covalent geometry : angle 0.57681 (36900) hydrogen bonds : bond 0.03333 ( 1308) hydrogen bonds : angle 4.36142 ( 3753) Misc. bond : bond 0.00043 ( 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 388 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.9176 (tp) cc_final: 0.8968 (tp) REVERT: A 371 MET cc_start: 0.8053 (mmt) cc_final: 0.7786 (mmm) REVERT: A 546 CYS cc_start: 0.8739 (m) cc_final: 0.8397 (m) REVERT: B 240 LEU cc_start: 0.8509 (tp) cc_final: 0.7923 (tp) REVERT: B 305 ASP cc_start: 0.8873 (p0) cc_final: 0.8659 (p0) REVERT: B 319 GLU cc_start: 0.7928 (pm20) cc_final: 0.7662 (pm20) REVERT: B 401 LYS cc_start: 0.9174 (mttt) cc_final: 0.8839 (tppt) REVERT: B 546 CYS cc_start: 0.8766 (m) cc_final: 0.8313 (m) REVERT: B 740 MET cc_start: 0.8784 (tmm) cc_final: 0.8377 (tmm) REVERT: C 318 MET cc_start: 0.8612 (tmm) cc_final: 0.8181 (tmm) REVERT: C 369 MET cc_start: 0.8668 (ptm) cc_final: 0.8451 (ptt) REVERT: C 473 MET cc_start: 0.7556 (tpt) cc_final: 0.7225 (tpp) REVERT: C 493 SER cc_start: 0.9190 (m) cc_final: 0.8841 (p) REVERT: C 574 LYS cc_start: 0.8939 (ptmt) cc_final: 0.8655 (ptmt) REVERT: C 652 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7608 (pt0) REVERT: C 741 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7867 (tp-100) REVERT: D 204 ILE cc_start: 0.9096 (tt) cc_final: 0.8884 (pt) REVERT: D 231 MET cc_start: 0.6391 (mmm) cc_final: 0.5977 (tpt) REVERT: D 286 ASP cc_start: 0.7825 (t0) cc_final: 0.7569 (t0) REVERT: D 398 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 466 TRP cc_start: 0.6793 (p90) cc_final: 0.5875 (p90) REVERT: D 580 GLU cc_start: 0.8838 (mp0) cc_final: 0.8402 (mp0) REVERT: D 649 MET cc_start: 0.8253 (tpt) cc_final: 0.8012 (tpp) REVERT: D 740 MET cc_start: 0.8058 (tmm) cc_final: 0.7663 (tmm) REVERT: E 515 MET cc_start: 0.9012 (tpp) cc_final: 0.8477 (tpp) REVERT: E 626 LEU cc_start: 0.8755 (mm) cc_final: 0.8381 (mm) REVERT: E 628 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8428 (mm-30) REVERT: E 777 MET cc_start: 0.7348 (mmp) cc_final: 0.6737 (mmt) REVERT: F 217 GLU cc_start: 0.7469 (mp0) cc_final: 0.7258 (mp0) REVERT: F 303 GLU cc_start: 0.6410 (mp0) cc_final: 0.5866 (mp0) REVERT: F 367 ILE cc_start: 0.7232 (mt) cc_final: 0.6973 (mt) REVERT: F 369 MET cc_start: 0.2969 (mpp) cc_final: 0.2720 (mpp) REVERT: F 371 MET cc_start: 0.7525 (tmm) cc_final: 0.7226 (tmm) REVERT: F 585 GLN cc_start: 0.8691 (tt0) cc_final: 0.8485 (tp40) REVERT: F 603 MET cc_start: 0.8230 (tpp) cc_final: 0.7754 (tpp) REVERT: F 649 MET cc_start: 0.8207 (mpp) cc_final: 0.7996 (mpp) outliers start: 1 outliers final: 0 residues processed: 388 average time/residue: 0.1574 time to fit residues: 100.6396 Evaluate side-chains 296 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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: 0.6980 chunk 277 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078006 restraints weight = 69710.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080143 restraints weight = 42683.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.081591 restraints weight = 29777.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082593 restraints weight = 22930.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.083165 restraints weight = 19001.114| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27244 Z= 0.129 Angle : 0.570 10.934 36900 Z= 0.290 Chirality : 0.042 0.168 4196 Planarity : 0.005 0.089 4790 Dihedral : 9.572 85.310 4024 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.09 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 0.67 (0.15), residues: 3397 helix: 1.42 (0.12), residues: 1818 sheet: -0.25 (0.27), residues: 355 loop : -0.78 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 332 TYR 0.037 0.001 TYR D 752 PHE 0.024 0.002 PHE D 354 TRP 0.010 0.001 TRP D 453 HIS 0.005 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00294 (27242) covalent geometry : angle 0.56998 (36900) hydrogen bonds : bond 0.03191 ( 1308) hydrogen bonds : angle 4.27496 ( 3753) Misc. bond : bond 0.00031 ( 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 393 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.9172 (tp) cc_final: 0.8962 (tp) REVERT: A 318 MET cc_start: 0.5447 (tpt) cc_final: 0.4962 (tpp) REVERT: A 371 MET cc_start: 0.8065 (mmt) cc_final: 0.7836 (mmm) REVERT: A 546 CYS cc_start: 0.8639 (m) cc_final: 0.8304 (m) REVERT: B 240 LEU cc_start: 0.8501 (tp) cc_final: 0.7953 (tp) REVERT: B 319 GLU cc_start: 0.8001 (pm20) cc_final: 0.7742 (pm20) REVERT: B 401 LYS cc_start: 0.9164 (mttt) cc_final: 0.8808 (tppt) REVERT: B 546 CYS cc_start: 0.8735 (m) cc_final: 0.8281 (m) REVERT: B 740 MET cc_start: 0.8770 (tmm) cc_final: 0.8299 (tmm) REVERT: B 797 TYR cc_start: 0.7495 (m-80) cc_final: 0.6663 (m-80) REVERT: C 318 MET cc_start: 0.8601 (tmm) cc_final: 0.8120 (tmm) REVERT: C 369 MET cc_start: 0.8595 (ptm) cc_final: 0.8357 (ptt) REVERT: C 493 SER cc_start: 0.9156 (m) cc_final: 0.8805 (p) REVERT: C 525 GLU cc_start: 0.8137 (pm20) cc_final: 0.7297 (mt-10) REVERT: C 652 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7528 (pt0) REVERT: C 741 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7784 (tp-100) REVERT: D 204 ILE cc_start: 0.9054 (tt) cc_final: 0.8841 (pt) REVERT: D 286 ASP cc_start: 0.7837 (t0) cc_final: 0.7554 (t0) REVERT: D 398 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8373 (mm-30) REVERT: D 466 TRP cc_start: 0.6729 (p90) cc_final: 0.5833 (p90) REVERT: D 580 GLU cc_start: 0.8797 (mp0) cc_final: 0.8381 (mp0) REVERT: D 649 MET cc_start: 0.8218 (tpt) cc_final: 0.7967 (tpp) REVERT: D 740 MET cc_start: 0.8102 (tmm) cc_final: 0.7694 (tmm) REVERT: E 299 ILE cc_start: 0.9124 (mm) cc_final: 0.8917 (pt) REVERT: E 515 MET cc_start: 0.9026 (tpp) cc_final: 0.8490 (tpp) REVERT: E 628 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8399 (mm-30) REVERT: E 777 MET cc_start: 0.7312 (mmp) cc_final: 0.6630 (mmt) REVERT: F 219 TRP cc_start: 0.6043 (t-100) cc_final: 0.5696 (t-100) REVERT: F 303 GLU cc_start: 0.6386 (mp0) cc_final: 0.5862 (mp0) REVERT: F 367 ILE cc_start: 0.7079 (mt) cc_final: 0.6859 (mt) REVERT: F 369 MET cc_start: 0.2888 (mpp) cc_final: 0.2633 (mpp) REVERT: F 371 MET cc_start: 0.7515 (tmm) cc_final: 0.7253 (tmm) REVERT: F 603 MET cc_start: 0.8169 (tpp) cc_final: 0.7880 (tpp) REVERT: F 649 MET cc_start: 0.8239 (mpp) cc_final: 0.8025 (mpp) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1509 time to fit residues: 99.3875 Evaluate side-chains 299 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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: 0.3980 chunk 183 optimal weight: 0.0670 chunk 314 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.078365 restraints weight = 70011.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080490 restraints weight = 43628.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081858 restraints weight = 30429.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082850 restraints weight = 23553.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083456 restraints weight = 19543.946| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27244 Z= 0.130 Angle : 0.575 13.779 36900 Z= 0.290 Chirality : 0.042 0.200 4196 Planarity : 0.005 0.071 4790 Dihedral : 9.479 85.741 4024 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.12 % Favored : 93.67 % 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: 0.67 (0.15), residues: 3397 helix: 1.44 (0.12), residues: 1820 sheet: -0.29 (0.27), residues: 355 loop : -0.79 (0.19), residues: 1222 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 0.020 0.002 PHE E 476 TRP 0.010 0.001 TRP D 453 HIS 0.006 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00300 (27242) covalent geometry : angle 0.57511 (36900) hydrogen bonds : bond 0.03140 ( 1308) hydrogen bonds : angle 4.23786 ( 3753) Misc. bond : bond 0.00031 ( 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 393 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.079 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: 0.9065 (mm-30) cc_final: 0.8862 (tp30) REVERT: A 318 MET cc_start: 0.5446 (tpt) cc_final: 0.4924 (tpp) REVERT: A 371 MET cc_start: 0.8090 (mmt) cc_final: 0.7859 (mmm) REVERT: A 546 CYS cc_start: 0.8597 (m) cc_final: 0.8201 (m) REVERT: A 772 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7428 (mm-30) REVERT: B 240 LEU cc_start: 0.8508 (tp) cc_final: 0.7945 (tp) REVERT: B 401 LYS cc_start: 0.9118 (mttt) cc_final: 0.8798 (tppt) REVERT: B 546 CYS cc_start: 0.8737 (m) cc_final: 0.8249 (m) REVERT: B 603 MET cc_start: 0.8193 (mmt) cc_final: 0.7883 (mmp) REVERT: B 740 MET cc_start: 0.8759 (tmm) cc_final: 0.8299 (tmm) REVERT: B 797 TYR cc_start: 0.7389 (m-80) cc_final: 0.6541 (m-80) REVERT: C 318 MET cc_start: 0.8653 (tmm) cc_final: 0.8128 (tmm) REVERT: C 369 MET cc_start: 0.8597 (ptm) cc_final: 0.8387 (ptt) REVERT: C 493 SER cc_start: 0.9156 (m) cc_final: 0.8808 (p) REVERT: C 525 GLU cc_start: 0.8104 (pm20) cc_final: 0.7191 (mt-10) REVERT: C 652 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7495 (pt0) REVERT: C 741 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7798 (tp-100) REVERT: D 204 ILE cc_start: 0.9067 (tt) cc_final: 0.8851 (pt) REVERT: D 231 MET cc_start: 0.6136 (mmm) cc_final: 0.5783 (tpt) REVERT: D 286 ASP cc_start: 0.7804 (t0) cc_final: 0.7585 (t0) REVERT: D 398 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8348 (mm-30) REVERT: D 466 TRP cc_start: 0.6744 (p90) cc_final: 0.5905 (p90) REVERT: D 580 GLU cc_start: 0.8783 (mp0) cc_final: 0.8344 (mp0) REVERT: D 649 MET cc_start: 0.8215 (tpt) cc_final: 0.7969 (tpp) REVERT: D 740 MET cc_start: 0.8075 (tmm) cc_final: 0.7666 (tmm) REVERT: E 515 MET cc_start: 0.9010 (tpp) cc_final: 0.8500 (tpp) REVERT: E 628 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8383 (mm-30) REVERT: E 777 MET cc_start: 0.7310 (mmp) cc_final: 0.6613 (mmt) REVERT: F 219 TRP cc_start: 0.6054 (t-100) cc_final: 0.5705 (t-100) REVERT: F 303 GLU cc_start: 0.6376 (mp0) cc_final: 0.5837 (mp0) REVERT: F 367 ILE cc_start: 0.7180 (mt) cc_final: 0.6941 (mt) REVERT: F 369 MET cc_start: 0.2866 (mpp) cc_final: 0.2600 (mpp) REVERT: F 371 MET cc_start: 0.7473 (tmm) cc_final: 0.7233 (tmm) REVERT: F 603 MET cc_start: 0.8100 (tpp) cc_final: 0.7833 (tpp) REVERT: F 649 MET cc_start: 0.8273 (mpp) cc_final: 0.8037 (mpp) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1533 time to fit residues: 100.0260 Evaluate side-chains 297 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 1.9990 chunk 287 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.076607 restraints weight = 70618.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.078611 restraints weight = 43813.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.079986 restraints weight = 30832.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080904 restraints weight = 23850.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081567 restraints weight = 19862.196| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27244 Z= 0.192 Angle : 0.624 10.798 36900 Z= 0.317 Chirality : 0.043 0.207 4196 Planarity : 0.005 0.101 4790 Dihedral : 9.622 88.892 4024 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 0.55 (0.15), residues: 3397 helix: 1.36 (0.12), residues: 1820 sheet: -0.30 (0.27), residues: 360 loop : -0.88 (0.19), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 477 TYR 0.033 0.002 TYR D 752 PHE 0.022 0.002 PHE B 476 TRP 0.011 0.001 TRP F 500 HIS 0.008 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00438 (27242) covalent geometry : angle 0.62444 (36900) hydrogen bonds : bond 0.03408 ( 1308) hydrogen bonds : angle 4.40280 ( 3753) Misc. bond : bond 0.00090 ( 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 380 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8886 (tp30) REVERT: A 318 MET cc_start: 0.5471 (tpt) cc_final: 0.4943 (tpp) REVERT: A 371 MET cc_start: 0.8105 (mmt) cc_final: 0.7861 (mmm) REVERT: A 539 LEU cc_start: 0.9548 (tp) cc_final: 0.9331 (tt) REVERT: A 546 CYS cc_start: 0.8662 (m) cc_final: 0.8322 (m) REVERT: A 566 ILE cc_start: 0.9630 (mm) cc_final: 0.9399 (mm) REVERT: A 772 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7314 (mm-30) REVERT: B 240 LEU cc_start: 0.8574 (tp) cc_final: 0.7977 (tp) REVERT: B 319 GLU cc_start: 0.7949 (pm20) cc_final: 0.7699 (pm20) REVERT: B 368 ASP cc_start: 0.8207 (p0) cc_final: 0.7931 (p0) REVERT: B 401 LYS cc_start: 0.9172 (mttt) cc_final: 0.8826 (tppt) REVERT: B 546 CYS cc_start: 0.8753 (m) cc_final: 0.8309 (m) REVERT: B 571 LEU cc_start: 0.9241 (mt) cc_final: 0.9035 (mt) REVERT: B 740 MET cc_start: 0.8805 (tmm) cc_final: 0.8413 (tmm) REVERT: B 797 TYR cc_start: 0.7467 (m-80) cc_final: 0.6581 (m-80) REVERT: C 318 MET cc_start: 0.8657 (tmm) cc_final: 0.8162 (tmm) REVERT: C 369 MET cc_start: 0.8607 (ptm) cc_final: 0.8367 (ptt) REVERT: C 473 MET cc_start: 0.7343 (ttt) cc_final: 0.6443 (tmm) REVERT: C 493 SER cc_start: 0.9199 (m) cc_final: 0.8843 (p) REVERT: C 574 LYS cc_start: 0.8919 (ptmt) cc_final: 0.8682 (ptmm) REVERT: C 652 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7456 (pt0) REVERT: D 204 ILE cc_start: 0.9120 (tt) cc_final: 0.8891 (pt) REVERT: D 231 MET cc_start: 0.6597 (mmm) cc_final: 0.6232 (tpt) REVERT: D 286 ASP cc_start: 0.7875 (t0) cc_final: 0.7607 (t0) REVERT: D 398 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8363 (mm-30) REVERT: D 466 TRP cc_start: 0.7005 (p90) cc_final: 0.5983 (p90) REVERT: D 473 MET cc_start: 0.8338 (mmm) cc_final: 0.8109 (mmm) REVERT: D 546 CYS cc_start: 0.8408 (m) cc_final: 0.8177 (m) REVERT: D 580 GLU cc_start: 0.8842 (mp0) cc_final: 0.8336 (mp0) REVERT: D 639 TYR cc_start: 0.9044 (m-80) cc_final: 0.8781 (m-80) REVERT: D 649 MET cc_start: 0.8292 (tpt) cc_final: 0.8030 (tpp) REVERT: D 740 MET cc_start: 0.8036 (tmm) cc_final: 0.7613 (tmm) REVERT: E 515 MET cc_start: 0.9021 (tpp) cc_final: 0.8480 (tpp) REVERT: E 628 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8486 (mm-30) REVERT: F 219 TRP cc_start: 0.6130 (t-100) cc_final: 0.5750 (t-100) REVERT: F 367 ILE cc_start: 0.7189 (mt) cc_final: 0.6947 (mt) REVERT: F 369 MET cc_start: 0.2871 (mpp) cc_final: 0.2611 (mpp) REVERT: F 371 MET cc_start: 0.7511 (tmm) cc_final: 0.7265 (tmm) REVERT: F 603 MET cc_start: 0.8130 (tpp) cc_final: 0.7872 (tpp) REVERT: F 745 GLN cc_start: 0.8507 (mt0) cc_final: 0.8171 (mt0) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.1495 time to fit residues: 96.1437 Evaluate side-chains 296 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 217 optimal weight: 0.0470 chunk 195 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 ASN C 738 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.076280 restraints weight = 70377.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.078261 restraints weight = 43729.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.079548 restraints weight = 30887.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.080518 restraints weight = 24014.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.081113 restraints weight = 19971.479| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27244 Z= 0.194 Angle : 0.635 11.462 36900 Z= 0.322 Chirality : 0.043 0.199 4196 Planarity : 0.005 0.108 4790 Dihedral : 9.693 87.245 4024 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.01 % Favored : 92.82 % 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: 0.47 (0.15), residues: 3397 helix: 1.32 (0.12), residues: 1801 sheet: -0.36 (0.27), residues: 368 loop : -0.96 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 360 TYR 0.032 0.002 TYR D 752 PHE 0.019 0.002 PHE D 288 TRP 0.012 0.001 TRP C 219 HIS 0.007 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00441 (27242) covalent geometry : angle 0.63519 (36900) hydrogen bonds : bond 0.03434 ( 1308) hydrogen bonds : angle 4.45915 ( 3753) Misc. bond : bond 0.00087 ( 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 379 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.5493 (tpt) cc_final: 0.4971 (tpp) REVERT: A 371 MET cc_start: 0.8143 (mmt) cc_final: 0.7931 (mmm) REVERT: A 539 LEU cc_start: 0.9557 (tp) cc_final: 0.9316 (tt) REVERT: A 546 CYS cc_start: 0.8712 (m) cc_final: 0.8383 (m) REVERT: A 772 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7230 (mp0) REVERT: B 240 LEU cc_start: 0.8646 (tp) cc_final: 0.7990 (tp) REVERT: B 319 GLU cc_start: 0.8048 (pm20) cc_final: 0.7797 (pm20) REVERT: B 368 ASP cc_start: 0.8219 (p0) cc_final: 0.7948 (p0) REVERT: B 401 LYS cc_start: 0.9144 (mttt) cc_final: 0.8814 (tppt) REVERT: B 546 CYS cc_start: 0.8740 (m) cc_final: 0.8287 (m) REVERT: B 571 LEU cc_start: 0.9242 (mt) cc_final: 0.9037 (mt) REVERT: B 740 MET cc_start: 0.8824 (tmm) cc_final: 0.8409 (tmm) REVERT: B 797 TYR cc_start: 0.7463 (m-80) cc_final: 0.6525 (m-80) REVERT: C 318 MET cc_start: 0.8677 (tmm) cc_final: 0.8193 (tmm) REVERT: C 369 MET cc_start: 0.8608 (ptm) cc_final: 0.8376 (ptt) REVERT: C 493 SER cc_start: 0.9207 (m) cc_final: 0.8889 (p) REVERT: C 525 GLU cc_start: 0.8146 (pm20) cc_final: 0.7157 (mt-10) REVERT: C 652 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7444 (pt0) REVERT: D 286 ASP cc_start: 0.7882 (t0) cc_final: 0.7617 (t0) REVERT: D 473 MET cc_start: 0.8351 (mmm) cc_final: 0.8065 (mmm) REVERT: D 546 CYS cc_start: 0.8426 (m) cc_final: 0.8010 (m) REVERT: D 550 LEU cc_start: 0.8816 (pp) cc_final: 0.8568 (tp) REVERT: D 580 GLU cc_start: 0.8834 (mp0) cc_final: 0.8340 (mp0) REVERT: D 649 MET cc_start: 0.8317 (tpt) cc_final: 0.8076 (tpp) REVERT: D 740 MET cc_start: 0.8052 (tmm) cc_final: 0.7622 (tmm) REVERT: E 304 ILE cc_start: 0.9216 (tp) cc_final: 0.8991 (tp) REVERT: E 515 MET cc_start: 0.9009 (tpp) cc_final: 0.8460 (tpp) REVERT: E 628 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8495 (mm-30) REVERT: F 219 TRP cc_start: 0.6088 (t-100) cc_final: 0.5761 (t-100) REVERT: F 303 GLU cc_start: 0.6438 (mp0) cc_final: 0.5946 (mp0) REVERT: F 369 MET cc_start: 0.2724 (mpp) cc_final: 0.2469 (mpp) REVERT: F 371 MET cc_start: 0.7563 (tmm) cc_final: 0.7314 (tmm) REVERT: F 515 MET cc_start: 0.8600 (ppp) cc_final: 0.8131 (ppp) REVERT: F 603 MET cc_start: 0.8149 (tpp) cc_final: 0.7902 (tpp) REVERT: F 649 MET cc_start: 0.8249 (mpp) cc_final: 0.7941 (mpp) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1473 time to fit residues: 94.1494 Evaluate side-chains 297 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 5.9990 chunk 176 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 242 optimal weight: 0.0070 chunk 63 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 300 optimal weight: 5.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN B 459 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 ASN C 645 ASN C 738 ASN ** 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 = 0.3356 r_free = 0.3356 target = 0.097372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.076519 restraints weight = 70066.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.078521 restraints weight = 43541.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.079857 restraints weight = 30659.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.080733 restraints weight = 23832.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081414 restraints weight = 19969.634| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27244 Z= 0.179 Angle : 0.628 11.445 36900 Z= 0.316 Chirality : 0.043 0.260 4196 Planarity : 0.005 0.104 4790 Dihedral : 9.684 88.104 4024 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.98 % Favored : 92.85 % 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: 0.50 (0.15), residues: 3397 helix: 1.33 (0.12), residues: 1813 sheet: -0.32 (0.27), residues: 368 loop : -0.95 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 361 TYR 0.018 0.001 TYR D 752 PHE 0.016 0.002 PHE A 587 TRP 0.012 0.001 TRP C 219 HIS 0.006 0.001 HIS F 438 Details of bonding type rmsd covalent geometry : bond 0.00410 (27242) covalent geometry : angle 0.62808 (36900) hydrogen bonds : bond 0.03372 ( 1308) hydrogen bonds : angle 4.42762 ( 3753) Misc. bond : bond 0.00072 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3626.18 seconds wall clock time: 63 minutes 48.82 seconds (3828.82 seconds total)