Starting phenix.real_space_refine on Sat Feb 17 07:42:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlt_24540/02_2024/7rlt_24540_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 4 5.49 5 S 96 5.16 5 C 11432 2.51 5 N 3060 2.21 5 O 3404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A ARG 894": "NH1" <-> "NH2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 653": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C GLU 752": "OE1" <-> "OE2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C GLU 831": "OE1" <-> "OE2" Residue "C ARG 894": "NH1" <-> "NH2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B GLU 752": "OE1" <-> "OE2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ARG 894": "NH1" <-> "NH2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D GLU 730": "OE1" <-> "OE2" Residue "D GLU 752": "OE1" <-> "OE2" Residue "D GLU 768": "OE1" <-> "OE2" Residue "D GLU 831": "OE1" <-> "OE2" Residue "D ARG 894": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17996 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4478 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "C" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4478 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4478 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "D" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4478 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'PNS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'PNS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Time building chain proxies: 9.72, per 1000 atoms: 0.54 Number of scatterers: 17996 At special positions: 0 Unit cell: (100.32, 106.92, 117.48, 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 96 16.00 P 4 15.00 O 3404 8.00 N 3060 7.00 C 11432 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 - 3.50 Amino acid : False - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 3.4 seconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 24 sheets defined 43.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.517A pdb=" N ALA A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 351 No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 354 through 367 removed outlier: 3.745A pdb=" N VAL A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.528A pdb=" N TYR A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.605A pdb=" N LYS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.605A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 479 No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.623A pdb=" N LYS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 removed outlier: 4.816A pdb=" N ASP A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 590 removed outlier: 3.509A pdb=" N LYS A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 586 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 4.000A pdb=" N LEU A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 removed outlier: 3.967A pdb=" N GLN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.778A pdb=" N HIS A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 659 " --> pdb=" O GLY A 655 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN A 666 " --> pdb=" O CYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.812A pdb=" N GLN A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 721 through 733 removed outlier: 3.625A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 768 removed outlier: 3.801A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 802 No H-bonds generated for 'chain 'A' and resid 799 through 802' Processing helix chain 'A' and resid 820 through 828 Processing helix chain 'A' and resid 843 through 852 Processing helix chain 'A' and resid 886 through 892 removed outlier: 4.037A pdb=" N ASN A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 892 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 892' Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.502A pdb=" N ALA C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 351 No H-bonds generated for 'chain 'C' and resid 348 through 351' Processing helix chain 'C' and resid 354 through 367 removed outlier: 3.745A pdb=" N VAL C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 removed outlier: 3.520A pdb=" N TYR C 379 " --> pdb=" O ASN C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.585A pdb=" N LYS C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 473 removed outlier: 3.591A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 479 No H-bonds generated for 'chain 'C' and resid 476 through 479' Processing helix chain 'C' and resid 482 through 498 Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 515 through 520 removed outlier: 3.619A pdb=" N LYS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 539 removed outlier: 4.820A pdb=" N ASP C 538 " --> pdb=" O ALA C 534 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 590 removed outlier: 3.864A pdb=" N LEU C 580 " --> pdb=" O PRO C 576 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA C 586 " --> pdb=" O TRP C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 616 removed outlier: 4.010A pdb=" N LEU C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 615 " --> pdb=" O GLU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.958A pdb=" N GLN C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 638 " --> pdb=" O GLY C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.828A pdb=" N HIS C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN C 666 " --> pdb=" O CYS C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 699 removed outlier: 3.795A pdb=" N GLN C 693 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing helix chain 'C' and resid 721 through 733 removed outlier: 3.617A pdb=" N GLU C 729 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 768 removed outlier: 3.845A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 802 No H-bonds generated for 'chain 'C' and resid 799 through 802' Processing helix chain 'C' and resid 820 through 828 Processing helix chain 'C' and resid 843 through 852 Processing helix chain 'C' and resid 886 through 892 removed outlier: 4.055A pdb=" N ASN C 890 " --> pdb=" O GLU C 886 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU C 891 " --> pdb=" O ALA C 887 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR C 892 " --> pdb=" O ALA C 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 892' Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 348 through 351 No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 354 through 367 removed outlier: 3.741A pdb=" N VAL B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.529A pdb=" N TYR B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.577A pdb=" N LYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 473 removed outlier: 3.590A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 No H-bonds generated for 'chain 'B' and resid 476 through 479' Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.616A pdb=" N LYS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 539 removed outlier: 4.816A pdb=" N ASP B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 590 removed outlier: 3.851A pdb=" N LEU B 580 " --> pdb=" O PRO B 576 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 583 " --> pdb=" O MET B 579 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 586 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 removed outlier: 4.011A pdb=" N LEU B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 639 removed outlier: 3.972A pdb=" N GLN B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 3.843A pdb=" N HIS B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN B 666 " --> pdb=" O CYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.798A pdb=" N GLN B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 719 No H-bonds generated for 'chain 'B' and resid 717 through 719' Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.624A pdb=" N GLU B 729 " --> pdb=" O GLN B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 768 removed outlier: 3.821A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 820 through 828 Processing helix chain 'B' and resid 843 through 852 Processing helix chain 'B' and resid 886 through 892 removed outlier: 4.052A pdb=" N ASN B 890 " --> pdb=" O GLU B 886 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR B 892 " --> pdb=" O ALA B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 892' Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.510A pdb=" N ALA D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 351 No H-bonds generated for 'chain 'D' and resid 348 through 351' Processing helix chain 'D' and resid 354 through 367 removed outlier: 3.739A pdb=" N VAL D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 380 removed outlier: 3.534A pdb=" N TYR D 379 " --> pdb=" O ASN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 396 removed outlier: 3.602A pdb=" N LYS D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 473 removed outlier: 3.606A pdb=" N LYS D 463 " --> pdb=" O SER D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 479 No H-bonds generated for 'chain 'D' and resid 476 through 479' Processing helix chain 'D' and resid 482 through 498 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.611A pdb=" N LYS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 539 removed outlier: 4.810A pdb=" N ASP D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 590 removed outlier: 3.527A pdb=" N LYS D 583 " --> pdb=" O MET D 579 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 586 " --> pdb=" O TRP D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 616 removed outlier: 4.002A pdb=" N LEU D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS D 615 " --> pdb=" O GLU D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 639 removed outlier: 3.976A pdb=" N GLN D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 638 " --> pdb=" O GLY D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 removed outlier: 3.842A pdb=" N HIS D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 665 " --> pdb=" O SER D 661 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN D 666 " --> pdb=" O CYS D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.818A pdb=" N GLN D 693 " --> pdb=" O ASN D 689 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 699 " --> pdb=" O GLY D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 719 No H-bonds generated for 'chain 'D' and resid 717 through 719' Processing helix chain 'D' and resid 721 through 733 removed outlier: 3.624A pdb=" N GLU D 729 " --> pdb=" O GLN D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 767 removed outlier: 3.824A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 802 No H-bonds generated for 'chain 'D' and resid 799 through 802' Processing helix chain 'D' and resid 820 through 828 Processing helix chain 'D' and resid 843 through 852 Processing helix chain 'D' and resid 886 through 892 removed outlier: 4.046A pdb=" N ASN D 890 " --> pdb=" O GLU D 886 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 891 " --> pdb=" O ALA D 887 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 892 " --> pdb=" O ALA D 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 886 through 892' Processing sheet with id= A, first strand: chain 'A' and resid 408 through 412 removed outlier: 3.767A pdb=" N MET A 420 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 438 through 440 Processing sheet with id= C, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.589A pdb=" N ALA A 543 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 557 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.814A pdb=" N LYS A 645 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS A 669 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE A 648 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N SER A 671 " --> pdb=" O PHE A 648 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 594 through 596 Processing sheet with id= F, first strand: chain 'A' and resid 857 through 860 removed outlier: 7.686A pdb=" N LEU A 713 " --> pdb=" O ILE A 809 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 811 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 715 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N SER A 813 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 789 " --> pdb=" O MET A 810 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE A 812 " --> pdb=" O THR A 789 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE A 791 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ARG A 814 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS A 774 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR A 792 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU A 772 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.797A pdb=" N MET C 420 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 438 through 440 Processing sheet with id= I, first strand: chain 'C' and resid 543 through 545 removed outlier: 3.600A pdb=" N ALA C 543 " --> pdb=" O THR C 559 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR C 557 " --> pdb=" O ILE C 545 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 567 through 569 removed outlier: 6.813A pdb=" N LYS C 645 " --> pdb=" O GLY C 568 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 594 through 596 Processing sheet with id= L, first strand: chain 'C' and resid 857 through 860 removed outlier: 7.710A pdb=" N LEU C 713 " --> pdb=" O ILE C 809 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 811 " --> pdb=" O LEU C 713 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL C 715 " --> pdb=" O ILE C 811 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER C 813 " --> pdb=" O VAL C 715 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR C 789 " --> pdb=" O MET C 810 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE C 812 " --> pdb=" O THR C 789 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE C 791 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG C 814 " --> pdb=" O PHE C 791 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 408 through 412 removed outlier: 3.798A pdb=" N MET B 420 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 438 through 440 Processing sheet with id= O, first strand: chain 'B' and resid 543 through 545 removed outlier: 3.623A pdb=" N ALA B 543 " --> pdb=" O THR B 559 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR B 557 " --> pdb=" O ILE B 545 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 567 through 569 removed outlier: 6.832A pdb=" N LYS B 645 " --> pdb=" O GLY B 568 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 594 through 596 Processing sheet with id= R, first strand: chain 'B' and resid 857 through 860 removed outlier: 7.721A pdb=" N LEU B 713 " --> pdb=" O ILE B 809 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 811 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL B 715 " --> pdb=" O ILE B 811 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER B 813 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 789 " --> pdb=" O MET B 810 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B 812 " --> pdb=" O THR B 789 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 791 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ARG B 814 " --> pdb=" O PHE B 791 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS B 774 " --> pdb=" O VAL B 790 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR B 792 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU B 772 " --> pdb=" O THR B 792 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 408 through 412 removed outlier: 3.770A pdb=" N MET D 420 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 438 through 440 Processing sheet with id= U, first strand: chain 'D' and resid 543 through 545 removed outlier: 3.602A pdb=" N ALA D 543 " --> pdb=" O THR D 559 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR D 557 " --> pdb=" O ILE D 545 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 567 through 569 removed outlier: 6.817A pdb=" N LYS D 645 " --> pdb=" O GLY D 568 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 594 through 596 Processing sheet with id= X, first strand: chain 'D' and resid 857 through 860 removed outlier: 7.723A pdb=" N LEU D 713 " --> pdb=" O ILE D 809 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE D 811 " --> pdb=" O LEU D 713 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL D 715 " --> pdb=" O ILE D 811 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER D 813 " --> pdb=" O VAL D 715 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR D 789 " --> pdb=" O MET D 810 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE D 812 " --> pdb=" O THR D 789 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE D 791 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ARG D 814 " --> pdb=" O PHE D 791 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N CYS D 774 " --> pdb=" O VAL D 790 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR D 792 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU D 772 " --> pdb=" O THR D 792 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1836 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: 6.33 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5009 1.34 - 1.46: 2859 1.46 - 1.58: 10300 1.58 - 1.70: 4 1.70 - 1.82: 148 Bond restraints: 18320 Sorted by residual: bond pdb=" C39 PNS B1001 " pdb=" N41 PNS B1001 " ideal model delta sigma weight residual 1.452 1.333 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C39 PNS B1002 " pdb=" N41 PNS B1002 " ideal model delta sigma weight residual 1.452 1.333 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C39 PNS A1002 " pdb=" N41 PNS A1002 " ideal model delta sigma weight residual 1.452 1.333 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C39 PNS A1001 " pdb=" N41 PNS A1001 " ideal model delta sigma weight residual 1.452 1.333 0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C34 PNS B1001 " pdb=" N36 PNS B1001 " ideal model delta sigma weight residual 1.452 1.338 0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 18315 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.44: 455 106.44 - 113.41: 9601 113.41 - 120.38: 7620 120.38 - 127.35: 7027 127.35 - 134.32: 85 Bond angle restraints: 24788 Sorted by residual: angle pdb=" C VAL D 654 " pdb=" N GLY D 655 " pdb=" CA GLY D 655 " ideal model delta sigma weight residual 119.98 124.43 -4.45 1.11e+00 8.12e-01 1.61e+01 angle pdb=" C VAL B 633 " pdb=" N GLY B 634 " pdb=" CA GLY B 634 " ideal model delta sigma weight residual 119.98 124.42 -4.44 1.11e+00 8.12e-01 1.60e+01 angle pdb=" C VAL C 633 " pdb=" N GLY C 634 " pdb=" CA GLY C 634 " ideal model delta sigma weight residual 119.98 124.41 -4.43 1.11e+00 8.12e-01 1.59e+01 angle pdb=" C VAL B 654 " pdb=" N GLY B 655 " pdb=" CA GLY B 655 " ideal model delta sigma weight residual 120.00 124.39 -4.39 1.10e+00 8.26e-01 1.59e+01 angle pdb=" C VAL C 654 " pdb=" N GLY C 655 " pdb=" CA GLY C 655 " ideal model delta sigma weight residual 120.00 124.34 -4.34 1.10e+00 8.26e-01 1.56e+01 ... (remaining 24783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 10037 17.89 - 35.79: 742 35.79 - 53.68: 171 53.68 - 71.58: 41 71.58 - 89.47: 9 Dihedral angle restraints: 11000 sinusoidal: 4364 harmonic: 6636 Sorted by residual: dihedral pdb=" CA PRO A 871 " pdb=" C PRO A 871 " pdb=" N PHE A 872 " pdb=" CA PHE A 872 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PRO D 871 " pdb=" C PRO D 871 " pdb=" N PHE D 872 " pdb=" CA PHE D 872 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PRO C 603 " pdb=" C PRO C 603 " pdb=" N LEU C 604 " pdb=" CA LEU C 604 " ideal model delta harmonic sigma weight residual 180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 10997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1103 0.038 - 0.075: 744 0.075 - 0.113: 757 0.113 - 0.151: 199 0.151 - 0.188: 17 Chirality restraints: 2820 Sorted by residual: chirality pdb=" CB VAL A 338 " pdb=" CA VAL A 338 " pdb=" CG1 VAL A 338 " pdb=" CG2 VAL A 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CB VAL C 338 " pdb=" CA VAL C 338 " pdb=" CG1 VAL C 338 " pdb=" CG2 VAL C 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB VAL D 338 " pdb=" CA VAL D 338 " pdb=" CG1 VAL D 338 " pdb=" CG2 VAL D 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 2817 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 781 " -0.245 9.50e-02 1.11e+02 1.10e-01 7.41e+00 pdb=" NE ARG C 781 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 781 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 781 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 781 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 531 " 0.151 9.50e-02 1.11e+02 6.76e-02 2.86e+00 pdb=" NE ARG B 531 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 531 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 531 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 531 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 531 " 0.149 9.50e-02 1.11e+02 6.70e-02 2.80e+00 pdb=" NE ARG A 531 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 531 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 531 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 531 " 0.004 2.00e-02 2.50e+03 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 8014 2.99 - 3.47: 19054 3.47 - 3.95: 30520 3.95 - 4.42: 35531 4.42 - 4.90: 58076 Nonbonded interactions: 151195 Sorted by model distance: nonbonded pdb=" O MET B 696 " pdb=" N PHE B 700 " model vdw 2.518 2.520 nonbonded pdb=" O MET D 696 " pdb=" N PHE D 700 " model vdw 2.518 2.520 nonbonded pdb=" O MET C 696 " pdb=" N PHE C 700 " model vdw 2.520 2.520 nonbonded pdb=" O MET A 696 " pdb=" N PHE A 700 " model vdw 2.525 2.520 nonbonded pdb=" O MET B 525 " pdb=" OG1 THR B 529 " model vdw 2.528 2.440 ... (remaining 151190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 315 through 902) selection = (chain 'B' and resid 315 through 902) selection = chain 'C' selection = chain 'D' } 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=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 1.850 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 49.410 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.009 0.119 18320 Z= 0.572 Angle : 1.265 10.657 24788 Z= 0.860 Chirality : 0.068 0.188 2820 Planarity : 0.006 0.110 3212 Dihedral : 13.914 89.471 6736 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 1.00 % Allowed : 10.27 % Favored : 88.73 % Rotamer: Outliers : 1.61 % Allowed : 4.11 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.14), residues: 2308 helix: -1.88 (0.12), residues: 940 sheet: -3.43 (0.23), residues: 364 loop : -3.21 (0.15), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 477 HIS 0.004 0.002 HIS B 657 PHE 0.013 0.002 PHE A 872 TYR 0.009 0.002 TYR D 902 ARG 0.004 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 643 time to evaluate : 1.981 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 332 MET cc_start: 0.7645 (mmt) cc_final: 0.7432 (mmm) REVERT: A 363 GLU cc_start: 0.7547 (tp30) cc_final: 0.7197 (mm-30) REVERT: A 365 LYS cc_start: 0.6992 (mtpt) cc_final: 0.5770 (pttp) REVERT: A 384 PHE cc_start: 0.7761 (t80) cc_final: 0.7486 (t80) REVERT: A 410 GLU cc_start: 0.7320 (tt0) cc_final: 0.7075 (mm-30) REVERT: A 415 LYS cc_start: 0.7019 (mttt) cc_final: 0.6257 (ptpt) REVERT: A 416 LEU cc_start: 0.7977 (mt) cc_final: 0.7698 (mt) REVERT: A 422 TYR cc_start: 0.6015 (p90) cc_final: 0.5755 (p90) REVERT: A 445 THR cc_start: 0.7673 (m) cc_final: 0.7273 (t) REVERT: A 446 ASP cc_start: 0.6926 (m-30) cc_final: 0.6651 (m-30) REVERT: A 548 ASN cc_start: 0.7413 (m-40) cc_final: 0.6594 (m-40) REVERT: A 562 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7083 (mm-30) REVERT: A 602 THR cc_start: 0.9049 (p) cc_final: 0.8648 (t) REVERT: A 620 LYS cc_start: 0.7570 (mttt) cc_final: 0.7180 (ptmt) REVERT: A 690 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7463 (tptp) REVERT: A 696 MET cc_start: 0.6852 (mtm) cc_final: 0.6391 (mtp) REVERT: A 702 ASN cc_start: 0.7601 (t0) cc_final: 0.7314 (t0) REVERT: A 703 LYS cc_start: 0.7735 (pttp) cc_final: 0.7238 (pttm) REVERT: A 725 GLN cc_start: 0.6624 (tm-30) cc_final: 0.6356 (tm-30) REVERT: A 744 THR cc_start: 0.8684 (m) cc_final: 0.8302 (m) REVERT: A 745 ASN cc_start: 0.7302 (m-40) cc_final: 0.7088 (m110) REVERT: A 761 TYR cc_start: 0.7576 (t80) cc_final: 0.7367 (t80) REVERT: A 763 GLN cc_start: 0.7871 (mt0) cc_final: 0.7563 (mt0) REVERT: A 784 PHE cc_start: 0.7351 (m-10) cc_final: 0.6599 (m-10) REVERT: A 804 GLU cc_start: 0.7166 (tt0) cc_final: 0.6893 (tt0) REVERT: A 824 LEU cc_start: 0.8415 (mt) cc_final: 0.7919 (mp) REVERT: A 848 TYR cc_start: 0.8343 (t80) cc_final: 0.7864 (t80) REVERT: A 852 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7876 (mmtt) REVERT: A 876 LYS cc_start: 0.6792 (mtmt) cc_final: 0.6590 (mtmm) REVERT: C 332 MET cc_start: 0.7671 (mmt) cc_final: 0.7111 (tpp) REVERT: C 363 GLU cc_start: 0.7538 (tp30) cc_final: 0.7169 (mm-30) REVERT: C 365 LYS cc_start: 0.6868 (mtpt) cc_final: 0.5722 (pttp) REVERT: C 384 PHE cc_start: 0.7749 (t80) cc_final: 0.7464 (t80) REVERT: C 410 GLU cc_start: 0.7156 (tt0) cc_final: 0.6804 (mm-30) REVERT: C 414 ASN cc_start: 0.6156 (t0) cc_final: 0.5930 (t0) REVERT: C 415 LYS cc_start: 0.7040 (mttt) cc_final: 0.6243 (ptpt) REVERT: C 422 TYR cc_start: 0.5899 (p90) cc_final: 0.5640 (p90) REVERT: C 434 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5652 (pt0) REVERT: C 445 THR cc_start: 0.7706 (m) cc_final: 0.7397 (t) REVERT: C 446 ASP cc_start: 0.6919 (m-30) cc_final: 0.6663 (m-30) REVERT: C 507 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 548 ASN cc_start: 0.7379 (m-40) cc_final: 0.6715 (m-40) REVERT: C 562 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7005 (mm-30) REVERT: C 602 THR cc_start: 0.9161 (p) cc_final: 0.8734 (t) REVERT: C 620 LYS cc_start: 0.7720 (mttt) cc_final: 0.7190 (ptmt) REVERT: C 666 ASN cc_start: 0.7578 (p0) cc_final: 0.6512 (p0) REVERT: C 690 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7599 (tptp) REVERT: C 696 MET cc_start: 0.6863 (mtm) cc_final: 0.6458 (mtp) REVERT: C 702 ASN cc_start: 0.7679 (t0) cc_final: 0.7305 (t0) REVERT: C 703 LYS cc_start: 0.7652 (pttp) cc_final: 0.7338 (pttm) REVERT: C 717 GLU cc_start: 0.7961 (tt0) cc_final: 0.7755 (tt0) REVERT: C 725 GLN cc_start: 0.6586 (tm-30) cc_final: 0.6304 (tm-30) REVERT: C 744 THR cc_start: 0.8674 (m) cc_final: 0.8319 (m) REVERT: C 745 ASN cc_start: 0.7456 (m-40) cc_final: 0.7237 (m110) REVERT: C 760 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7092 (tp30) REVERT: C 761 TYR cc_start: 0.7547 (t80) cc_final: 0.7324 (t80) REVERT: C 767 LYS cc_start: 0.6856 (tmtm) cc_final: 0.6471 (tptm) REVERT: C 784 PHE cc_start: 0.7597 (m-80) cc_final: 0.6906 (m-10) REVERT: C 799 TYR cc_start: 0.8022 (t80) cc_final: 0.7813 (t80) REVERT: C 803 GLU cc_start: 0.6780 (tp30) cc_final: 0.6573 (mm-30) REVERT: C 824 LEU cc_start: 0.8416 (mt) cc_final: 0.7891 (mp) REVERT: C 848 TYR cc_start: 0.8349 (t80) cc_final: 0.7745 (t80) REVERT: C 852 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7851 (mmtt) REVERT: C 876 LYS cc_start: 0.6838 (mtmt) cc_final: 0.6547 (mtmm) REVERT: C 894 ARG cc_start: 0.7943 (ptt180) cc_final: 0.7684 (ptt180) REVERT: B 332 MET cc_start: 0.7646 (mmt) cc_final: 0.7098 (tpp) REVERT: B 363 GLU cc_start: 0.7180 (tp30) cc_final: 0.6824 (mm-30) REVERT: B 365 LYS cc_start: 0.6884 (mtpt) cc_final: 0.5714 (pttp) REVERT: B 384 PHE cc_start: 0.7748 (t80) cc_final: 0.7464 (t80) REVERT: B 410 GLU cc_start: 0.7161 (tt0) cc_final: 0.6824 (mm-30) REVERT: B 414 ASN cc_start: 0.6151 (t0) cc_final: 0.5932 (t0) REVERT: B 415 LYS cc_start: 0.7044 (mttt) cc_final: 0.6247 (ptpt) REVERT: B 416 LEU cc_start: 0.7986 (mt) cc_final: 0.7708 (mt) REVERT: B 422 TYR cc_start: 0.5919 (p90) cc_final: 0.5683 (p90) REVERT: B 434 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5658 (pt0) REVERT: B 445 THR cc_start: 0.7699 (m) cc_final: 0.7361 (t) REVERT: B 446 ASP cc_start: 0.6937 (m-30) cc_final: 0.6658 (m-30) REVERT: B 494 ASP cc_start: 0.7685 (m-30) cc_final: 0.7308 (m-30) REVERT: B 528 GLN cc_start: 0.8033 (mt0) cc_final: 0.7768 (mt0) REVERT: B 562 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7063 (mm-30) REVERT: B 602 THR cc_start: 0.9165 (p) cc_final: 0.8746 (t) REVERT: B 620 LYS cc_start: 0.7718 (mttt) cc_final: 0.7184 (ptmt) REVERT: B 690 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7543 (tptp) REVERT: B 702 ASN cc_start: 0.7667 (t0) cc_final: 0.7078 (t0) REVERT: B 717 GLU cc_start: 0.7966 (tt0) cc_final: 0.7759 (tt0) REVERT: B 725 GLN cc_start: 0.6594 (tm-30) cc_final: 0.6315 (tm-30) REVERT: B 744 THR cc_start: 0.8672 (m) cc_final: 0.8305 (m) REVERT: B 745 ASN cc_start: 0.7453 (m-40) cc_final: 0.7242 (m110) REVERT: B 760 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6983 (tp30) REVERT: B 761 TYR cc_start: 0.7547 (t80) cc_final: 0.7309 (t80) REVERT: B 784 PHE cc_start: 0.7605 (m-80) cc_final: 0.6980 (m-10) REVERT: B 799 TYR cc_start: 0.7947 (t80) cc_final: 0.7650 (t80) REVERT: B 803 GLU cc_start: 0.6814 (tp30) cc_final: 0.6561 (mm-30) REVERT: B 824 LEU cc_start: 0.8421 (mt) cc_final: 0.7903 (mp) REVERT: B 848 TYR cc_start: 0.8341 (t80) cc_final: 0.7750 (t80) REVERT: B 852 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7847 (mmtt) REVERT: B 876 LYS cc_start: 0.6844 (mtmt) cc_final: 0.6587 (mtmm) REVERT: B 894 ARG cc_start: 0.7915 (ptt180) cc_final: 0.7675 (ptt180) REVERT: D 332 MET cc_start: 0.7633 (mmt) cc_final: 0.7079 (tpp) REVERT: D 363 GLU cc_start: 0.7274 (tp30) cc_final: 0.6967 (mm-30) REVERT: D 365 LYS cc_start: 0.7022 (mtpt) cc_final: 0.5770 (pttp) REVERT: D 384 PHE cc_start: 0.7778 (t80) cc_final: 0.7505 (t80) REVERT: D 410 GLU cc_start: 0.7133 (tt0) cc_final: 0.6785 (mm-30) REVERT: D 415 LYS cc_start: 0.7018 (mttt) cc_final: 0.6254 (ptpt) REVERT: D 416 LEU cc_start: 0.7987 (mt) cc_final: 0.7712 (mt) REVERT: D 419 GLN cc_start: 0.7328 (mt0) cc_final: 0.7053 (mt0) REVERT: D 422 TYR cc_start: 0.6117 (p90) cc_final: 0.5826 (p90) REVERT: D 445 THR cc_start: 0.7674 (m) cc_final: 0.7294 (t) REVERT: D 446 ASP cc_start: 0.6912 (m-30) cc_final: 0.6614 (m-30) REVERT: D 548 ASN cc_start: 0.7433 (m-40) cc_final: 0.6878 (m-40) REVERT: D 562 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7036 (mm-30) REVERT: D 602 THR cc_start: 0.9114 (p) cc_final: 0.8721 (t) REVERT: D 620 LYS cc_start: 0.7562 (mttt) cc_final: 0.7183 (ptmt) REVERT: D 648 PHE cc_start: 0.7195 (t80) cc_final: 0.6984 (t80) REVERT: D 690 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7412 (tptp) REVERT: D 696 MET cc_start: 0.6856 (mtm) cc_final: 0.6413 (mtp) REVERT: D 702 ASN cc_start: 0.7709 (t0) cc_final: 0.7509 (t0) REVERT: D 725 GLN cc_start: 0.6614 (tm-30) cc_final: 0.6339 (tm-30) REVERT: D 744 THR cc_start: 0.8691 (m) cc_final: 0.8324 (m) REVERT: D 745 ASN cc_start: 0.7310 (m-40) cc_final: 0.7082 (m110) REVERT: D 761 TYR cc_start: 0.7556 (t80) cc_final: 0.7331 (t80) REVERT: D 763 GLN cc_start: 0.7905 (mt0) cc_final: 0.7623 (mt0) REVERT: D 784 PHE cc_start: 0.7617 (m-80) cc_final: 0.6534 (m-10) REVERT: D 804 GLU cc_start: 0.7095 (tt0) cc_final: 0.6819 (tt0) REVERT: D 824 LEU cc_start: 0.8420 (mt) cc_final: 0.8121 (mm) REVERT: D 848 TYR cc_start: 0.8346 (t80) cc_final: 0.7852 (t80) REVERT: D 852 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7952 (mmtt) REVERT: D 876 LYS cc_start: 0.6736 (mtmt) cc_final: 0.6295 (mtmm) REVERT: D 883 ASP cc_start: 0.7525 (m-30) cc_final: 0.7248 (m-30) REVERT: D 894 ARG cc_start: 0.7913 (ptt180) cc_final: 0.7679 (ptt180) outliers start: 31 outliers final: 12 residues processed: 666 average time/residue: 0.3339 time to fit residues: 322.2825 Evaluate side-chains 445 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 431 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 751 HIS Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 751 HIS Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 703 LYS Chi-restraints excluded: chain D residue 751 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 chunk 118 optimal weight: 0.0470 chunk 93 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 overall best weight: 1.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 474 ASN A 745 ASN A 749 GLN A 750 ASN A 787 GLN A 844 ASN A 864 ASN A 877 GLN C 457 GLN C 474 ASN C 745 ASN C 750 ASN C 844 ASN B 457 GLN B 474 ASN B 600 GLN B 745 ASN B 750 ASN B 844 ASN D 457 GLN D 474 ASN D 745 ASN D 787 GLN D 844 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18320 Z= 0.182 Angle : 0.549 7.977 24788 Z= 0.286 Chirality : 0.039 0.174 2820 Planarity : 0.003 0.026 3212 Dihedral : 7.139 75.410 2544 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.54 % Rotamer: Outliers : 2.96 % Allowed : 11.95 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2308 helix: 0.38 (0.15), residues: 996 sheet: -3.14 (0.24), residues: 384 loop : -2.43 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 573 HIS 0.003 0.001 HIS C 797 PHE 0.017 0.002 PHE B 872 TYR 0.016 0.001 TYR B 408 ARG 0.004 0.001 ARG B 781 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 499 time to evaluate : 2.223 Fit side-chains revert: symmetry clash REVERT: A 332 MET cc_start: 0.7828 (mmt) cc_final: 0.7592 (mmm) REVERT: A 376 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6361 (tp30) REVERT: A 385 ARG cc_start: 0.7353 (ptm160) cc_final: 0.6126 (mpp80) REVERT: A 410 GLU cc_start: 0.7155 (tt0) cc_final: 0.6934 (mm-30) REVERT: A 414 ASN cc_start: 0.6483 (t0) cc_final: 0.5974 (t0) REVERT: A 415 LYS cc_start: 0.7106 (mttt) cc_final: 0.6450 (ptpt) REVERT: A 487 ARG cc_start: 0.6738 (tpt170) cc_final: 0.6403 (tpt-90) REVERT: A 507 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8356 (tp30) REVERT: A 562 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6956 (mt-10) REVERT: A 602 THR cc_start: 0.9112 (p) cc_final: 0.8632 (t) REVERT: A 620 LYS cc_start: 0.7730 (mttt) cc_final: 0.6876 (pptt) REVERT: A 639 ASP cc_start: 0.7018 (m-30) cc_final: 0.6611 (m-30) REVERT: A 666 ASN cc_start: 0.7064 (p0) cc_final: 0.6511 (p0) REVERT: A 690 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7339 (tttm) REVERT: A 702 ASN cc_start: 0.7656 (t0) cc_final: 0.7286 (t0) REVERT: A 712 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7720 (mtm180) REVERT: A 725 GLN cc_start: 0.6644 (tm-30) cc_final: 0.6433 (tm-30) REVERT: A 761 TYR cc_start: 0.7815 (t80) cc_final: 0.7041 (t80) REVERT: A 784 PHE cc_start: 0.7776 (m-80) cc_final: 0.7174 (m-10) REVERT: A 852 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7761 (mmtt) REVERT: C 332 MET cc_start: 0.7785 (mmt) cc_final: 0.7583 (mmm) REVERT: C 340 GLU cc_start: 0.6011 (tt0) cc_final: 0.5784 (pm20) REVERT: C 376 GLU cc_start: 0.6515 (mm-30) cc_final: 0.6307 (tp30) REVERT: C 385 ARG cc_start: 0.7357 (ptm160) cc_final: 0.6137 (mpp80) REVERT: C 410 GLU cc_start: 0.7124 (tt0) cc_final: 0.6913 (mm-30) REVERT: C 415 LYS cc_start: 0.7213 (mttt) cc_final: 0.6846 (ttmt) REVERT: C 422 TYR cc_start: 0.5981 (p90) cc_final: 0.5754 (p90) REVERT: C 434 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5731 (pt0) REVERT: C 487 ARG cc_start: 0.6709 (tpt170) cc_final: 0.6451 (tpt-90) REVERT: C 562 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7035 (mt-10) REVERT: C 583 LYS cc_start: 0.7415 (mttm) cc_final: 0.7109 (mttm) REVERT: C 602 THR cc_start: 0.9146 (p) cc_final: 0.8652 (t) REVERT: C 620 LYS cc_start: 0.7802 (mttt) cc_final: 0.6857 (pptt) REVERT: C 639 ASP cc_start: 0.6986 (m-30) cc_final: 0.6667 (m-30) REVERT: C 648 PHE cc_start: 0.7547 (t80) cc_final: 0.7340 (t80) REVERT: C 664 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3211 (pp) REVERT: C 690 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7105 (tttm) REVERT: C 702 ASN cc_start: 0.7757 (t0) cc_final: 0.7244 (t0) REVERT: C 725 GLN cc_start: 0.6621 (tm-30) cc_final: 0.6055 (tm-30) REVERT: C 754 HIS cc_start: 0.7619 (t70) cc_final: 0.7016 (t70) REVERT: C 757 LYS cc_start: 0.8260 (tmtt) cc_final: 0.8055 (ptmm) REVERT: C 784 PHE cc_start: 0.7845 (m-80) cc_final: 0.7184 (m-10) REVERT: C 799 TYR cc_start: 0.8314 (t80) cc_final: 0.8078 (t80) REVERT: C 803 GLU cc_start: 0.6843 (tp30) cc_final: 0.6562 (mm-30) REVERT: C 852 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7390 (mmtt) REVERT: B 332 MET cc_start: 0.7640 (mmt) cc_final: 0.7430 (mmm) REVERT: B 365 LYS cc_start: 0.6854 (mtpt) cc_final: 0.5771 (pttp) REVERT: B 366 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 376 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6294 (tp30) REVERT: B 385 ARG cc_start: 0.7358 (ptm160) cc_final: 0.6142 (mpp80) REVERT: B 410 GLU cc_start: 0.7123 (tt0) cc_final: 0.6920 (mm-30) REVERT: B 415 LYS cc_start: 0.7106 (mttt) cc_final: 0.6774 (mttt) REVERT: B 434 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5733 (pt0) REVERT: B 487 ARG cc_start: 0.6706 (tpt170) cc_final: 0.6441 (tpt-90) REVERT: B 562 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7114 (mt-10) REVERT: B 602 THR cc_start: 0.9130 (p) cc_final: 0.8629 (t) REVERT: B 607 LEU cc_start: 0.7650 (mt) cc_final: 0.7445 (mt) REVERT: B 620 LYS cc_start: 0.7826 (mttt) cc_final: 0.6879 (pptt) REVERT: B 639 ASP cc_start: 0.7096 (m-30) cc_final: 0.6612 (m-30) REVERT: B 690 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7035 (tttm) REVERT: B 702 ASN cc_start: 0.7771 (t0) cc_final: 0.7229 (t0) REVERT: B 725 GLN cc_start: 0.6620 (tm-30) cc_final: 0.6009 (tm-30) REVERT: B 754 HIS cc_start: 0.7510 (t70) cc_final: 0.7073 (t70) REVERT: B 757 LYS cc_start: 0.8257 (tmtt) cc_final: 0.8051 (ptmm) REVERT: B 784 PHE cc_start: 0.7791 (m-80) cc_final: 0.7249 (m-10) REVERT: B 799 TYR cc_start: 0.8153 (t80) cc_final: 0.7897 (t80) REVERT: B 803 GLU cc_start: 0.6858 (tp30) cc_final: 0.6577 (mm-30) REVERT: B 852 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7246 (mmtt) REVERT: B 876 LYS cc_start: 0.6748 (mtmt) cc_final: 0.6528 (mtmm) REVERT: D 332 MET cc_start: 0.7729 (mmt) cc_final: 0.7459 (mmm) REVERT: D 365 LYS cc_start: 0.6955 (mtpt) cc_final: 0.6672 (mmtp) REVERT: D 366 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7187 (mm-30) REVERT: D 376 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6317 (tp30) REVERT: D 385 ARG cc_start: 0.7359 (ptm160) cc_final: 0.6148 (mpp80) REVERT: D 410 GLU cc_start: 0.7133 (tt0) cc_final: 0.6908 (mm-30) REVERT: D 414 ASN cc_start: 0.6489 (t0) cc_final: 0.6087 (t0) REVERT: D 415 LYS cc_start: 0.7093 (mttt) cc_final: 0.6502 (ptpt) REVERT: D 419 GLN cc_start: 0.7708 (mt0) cc_final: 0.7295 (mt0) REVERT: D 422 TYR cc_start: 0.5888 (p90) cc_final: 0.5660 (p90) REVERT: D 487 ARG cc_start: 0.6740 (tpt170) cc_final: 0.6399 (tpt-90) REVERT: D 507 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8352 (tp30) REVERT: D 562 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7060 (mt-10) REVERT: D 602 THR cc_start: 0.9054 (p) cc_final: 0.8593 (t) REVERT: D 620 LYS cc_start: 0.7735 (mttt) cc_final: 0.6876 (pptt) REVERT: D 639 ASP cc_start: 0.6995 (m-30) cc_final: 0.6685 (m-30) REVERT: D 664 LEU cc_start: 0.4320 (OUTLIER) cc_final: 0.4046 (pp) REVERT: D 690 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7314 (tttm) REVERT: D 702 ASN cc_start: 0.7631 (t0) cc_final: 0.7305 (t0) REVERT: D 725 GLN cc_start: 0.6639 (tm-30) cc_final: 0.6431 (tm-30) REVERT: D 784 PHE cc_start: 0.7632 (m-80) cc_final: 0.7095 (m-10) REVERT: D 830 THR cc_start: 0.6365 (t) cc_final: 0.6126 (t) REVERT: D 852 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7970 (mmtt) outliers start: 57 outliers final: 24 residues processed: 526 average time/residue: 0.3076 time to fit residues: 241.0983 Evaluate side-chains 406 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 378 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 751 HIS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 751 HIS Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 703 LYS Chi-restraints excluded: chain D residue 751 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 228 optimal weight: 0.0570 chunk 187 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 ASN C 745 ASN C 749 GLN ** C 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN B 745 ASN B 749 GLN ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN D 745 ASN D 749 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18320 Z= 0.238 Angle : 0.541 8.297 24788 Z= 0.279 Chirality : 0.040 0.169 2820 Planarity : 0.003 0.032 3212 Dihedral : 6.964 76.846 2542 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.37 % Favored : 93.41 % Rotamer: Outliers : 4.00 % Allowed : 15.96 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2308 helix: 0.80 (0.16), residues: 1012 sheet: -2.59 (0.27), residues: 364 loop : -2.06 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 582 HIS 0.006 0.001 HIS A 522 PHE 0.017 0.002 PHE B 872 TYR 0.010 0.002 TYR A 761 ARG 0.004 0.001 ARG D 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 402 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7955 (mmt) cc_final: 0.7289 (tpp) REVERT: A 365 LYS cc_start: 0.6858 (mmtp) cc_final: 0.6404 (tppt) REVERT: A 366 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 385 ARG cc_start: 0.7357 (ptm160) cc_final: 0.6138 (mpp80) REVERT: A 415 LYS cc_start: 0.7275 (mttt) cc_final: 0.6938 (ttmt) REVERT: A 487 ARG cc_start: 0.6751 (tpt170) cc_final: 0.6537 (tpt-90) REVERT: A 562 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7130 (mt-10) REVERT: A 602 THR cc_start: 0.9044 (p) cc_final: 0.8548 (t) REVERT: A 620 LYS cc_start: 0.7844 (mttt) cc_final: 0.6995 (pptt) REVERT: A 639 ASP cc_start: 0.7224 (m-30) cc_final: 0.6708 (m-30) REVERT: A 664 LEU cc_start: 0.3793 (OUTLIER) cc_final: 0.3533 (pp) REVERT: A 666 ASN cc_start: 0.6956 (p0) cc_final: 0.6594 (p0) REVERT: A 690 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7181 (tttm) REVERT: A 702 ASN cc_start: 0.7774 (t0) cc_final: 0.7175 (t0) REVERT: A 705 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 712 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7758 (mtm180) REVERT: A 761 TYR cc_start: 0.7844 (t80) cc_final: 0.7332 (t80) REVERT: A 784 PHE cc_start: 0.7877 (m-80) cc_final: 0.7479 (m-80) REVERT: A 845 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7602 (mmtm) REVERT: C 332 MET cc_start: 0.7817 (mmt) cc_final: 0.7527 (mmm) REVERT: C 365 LYS cc_start: 0.7108 (mmtp) cc_final: 0.6629 (tppt) REVERT: C 366 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7052 (mm-30) REVERT: C 415 LYS cc_start: 0.7222 (mttt) cc_final: 0.6874 (ttmt) REVERT: C 521 THR cc_start: 0.8544 (t) cc_final: 0.8344 (t) REVERT: C 562 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 602 THR cc_start: 0.9156 (p) cc_final: 0.8694 (t) REVERT: C 620 LYS cc_start: 0.7942 (mttt) cc_final: 0.7021 (pptt) REVERT: C 639 ASP cc_start: 0.7300 (m-30) cc_final: 0.6798 (m-30) REVERT: C 648 PHE cc_start: 0.7684 (t80) cc_final: 0.7376 (t80) REVERT: C 666 ASN cc_start: 0.7126 (p0) cc_final: 0.6710 (p0) REVERT: C 690 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7419 (tttm) REVERT: C 702 ASN cc_start: 0.7742 (t0) cc_final: 0.7302 (t0) REVERT: C 799 TYR cc_start: 0.8346 (t80) cc_final: 0.7941 (t80) REVERT: C 803 GLU cc_start: 0.6894 (tp30) cc_final: 0.6565 (mm-30) REVERT: C 806 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: C 845 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7716 (mmtm) REVERT: C 882 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7678 (mmtm) REVERT: B 332 MET cc_start: 0.7865 (mmt) cc_final: 0.7613 (mmm) REVERT: B 366 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7084 (mm-30) REVERT: B 410 GLU cc_start: 0.7141 (tt0) cc_final: 0.6938 (mm-30) REVERT: B 415 LYS cc_start: 0.7172 (mttt) cc_final: 0.6827 (mttt) REVERT: B 487 ARG cc_start: 0.6813 (tpt170) cc_final: 0.6574 (tpt-90) REVERT: B 562 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 602 THR cc_start: 0.9157 (p) cc_final: 0.8686 (t) REVERT: B 607 LEU cc_start: 0.7636 (mt) cc_final: 0.7348 (mt) REVERT: B 620 LYS cc_start: 0.7839 (mttt) cc_final: 0.6771 (pptt) REVERT: B 639 ASP cc_start: 0.7209 (m-30) cc_final: 0.6778 (m-30) REVERT: B 690 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7323 (tttm) REVERT: B 702 ASN cc_start: 0.7658 (t0) cc_final: 0.7222 (t0) REVERT: B 784 PHE cc_start: 0.7905 (m-10) cc_final: 0.7294 (m-10) REVERT: B 787 GLN cc_start: 0.6907 (mt0) cc_final: 0.6707 (tt0) REVERT: B 799 TYR cc_start: 0.8181 (t80) cc_final: 0.7701 (t80) REVERT: B 803 GLU cc_start: 0.6828 (tp30) cc_final: 0.6494 (mm-30) REVERT: B 806 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: B 882 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7641 (mmtm) REVERT: D 332 MET cc_start: 0.7812 (mmt) cc_final: 0.7463 (mmm) REVERT: D 366 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7040 (mm-30) REVERT: D 410 GLU cc_start: 0.7543 (tt0) cc_final: 0.7287 (mm-30) REVERT: D 415 LYS cc_start: 0.7196 (mttt) cc_final: 0.6868 (ttmt) REVERT: D 419 GLN cc_start: 0.7460 (mt0) cc_final: 0.7145 (mt0) REVERT: D 562 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7134 (mt-10) REVERT: D 602 THR cc_start: 0.9097 (p) cc_final: 0.8626 (t) REVERT: D 620 LYS cc_start: 0.7844 (mttt) cc_final: 0.6992 (pptt) REVERT: D 639 ASP cc_start: 0.7290 (m-30) cc_final: 0.6796 (m-30) REVERT: D 648 PHE cc_start: 0.7532 (t80) cc_final: 0.7314 (t80) REVERT: D 664 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4316 (pp) REVERT: D 690 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7171 (tttm) REVERT: D 702 ASN cc_start: 0.7586 (t0) cc_final: 0.7151 (t0) REVERT: D 761 TYR cc_start: 0.7853 (t80) cc_final: 0.7312 (t80) REVERT: D 784 PHE cc_start: 0.7806 (m-80) cc_final: 0.7184 (m-80) REVERT: D 845 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7584 (mmtm) REVERT: D 882 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7735 (mmtm) outliers start: 77 outliers final: 50 residues processed: 448 average time/residue: 0.3124 time to fit residues: 208.2385 Evaluate side-chains 410 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 356 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 751 HIS Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 817 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 0.4980 chunk 109 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 224 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN C 635 GLN C 657 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18320 Z= 0.160 Angle : 0.499 8.813 24788 Z= 0.254 Chirality : 0.039 0.164 2820 Planarity : 0.003 0.033 3212 Dihedral : 6.172 59.652 2528 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.20 % Favored : 94.58 % Rotamer: Outliers : 3.22 % Allowed : 17.67 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2308 helix: 1.15 (0.17), residues: 1008 sheet: -2.27 (0.28), residues: 364 loop : -1.99 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 582 HIS 0.002 0.000 HIS A 657 PHE 0.017 0.001 PHE D 872 TYR 0.010 0.001 TYR B 761 ARG 0.002 0.000 ARG D 554 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 369 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: A 332 MET cc_start: 0.7925 (mmt) cc_final: 0.7599 (mmm) REVERT: A 365 LYS cc_start: 0.6806 (mmtp) cc_final: 0.6451 (tppt) REVERT: A 366 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 415 LYS cc_start: 0.7217 (mttt) cc_final: 0.6661 (ptpt) REVERT: A 422 TYR cc_start: 0.5850 (p90) cc_final: 0.5238 (p90) REVERT: A 562 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7130 (mt-10) REVERT: A 602 THR cc_start: 0.9113 (p) cc_final: 0.8651 (t) REVERT: A 620 LYS cc_start: 0.7999 (mttt) cc_final: 0.7417 (pptt) REVERT: A 639 ASP cc_start: 0.7290 (m-30) cc_final: 0.6794 (m-30) REVERT: A 666 ASN cc_start: 0.6957 (p0) cc_final: 0.6660 (p0) REVERT: A 690 LYS cc_start: 0.7702 (mtpt) cc_final: 0.7148 (tttm) REVERT: A 702 ASN cc_start: 0.7622 (t0) cc_final: 0.7367 (t0) REVERT: A 705 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 712 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7774 (mtm180) REVERT: A 761 TYR cc_start: 0.7794 (t80) cc_final: 0.7372 (t80) REVERT: A 784 PHE cc_start: 0.7755 (m-80) cc_final: 0.7336 (m-80) REVERT: A 824 LEU cc_start: 0.7969 (mt) cc_final: 0.7604 (tp) REVERT: A 845 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7777 (mmtm) REVERT: C 332 MET cc_start: 0.7809 (mmt) cc_final: 0.7516 (mmm) REVERT: C 365 LYS cc_start: 0.7125 (mmtp) cc_final: 0.6758 (tppt) REVERT: C 366 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7331 (mm-30) REVERT: C 415 LYS cc_start: 0.7137 (mttt) cc_final: 0.6754 (mttt) REVERT: C 562 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7136 (mt-10) REVERT: C 620 LYS cc_start: 0.8254 (mttt) cc_final: 0.7172 (pptt) REVERT: C 635 GLN cc_start: 0.6085 (OUTLIER) cc_final: 0.5280 (tp-100) REVERT: C 639 ASP cc_start: 0.7369 (m-30) cc_final: 0.6897 (m-30) REVERT: C 666 ASN cc_start: 0.7028 (p0) cc_final: 0.6757 (p0) REVERT: C 690 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7104 (tttm) REVERT: C 702 ASN cc_start: 0.7734 (t0) cc_final: 0.7287 (t0) REVERT: C 752 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6285 (mt-10) REVERT: C 784 PHE cc_start: 0.7739 (m-80) cc_final: 0.7071 (m-80) REVERT: C 799 TYR cc_start: 0.8041 (t80) cc_final: 0.7733 (t80) REVERT: C 803 GLU cc_start: 0.7064 (tp30) cc_final: 0.6720 (mm-30) REVERT: C 806 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: C 824 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7650 (mp) REVERT: B 332 MET cc_start: 0.7820 (mmt) cc_final: 0.7531 (mmm) REVERT: B 365 LYS cc_start: 0.7033 (tppt) cc_final: 0.6736 (tppt) REVERT: B 366 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 376 GLU cc_start: 0.6402 (tp30) cc_final: 0.6019 (tm-30) REVERT: B 380 MET cc_start: 0.6453 (ptp) cc_final: 0.6101 (ptm) REVERT: B 410 GLU cc_start: 0.7107 (tt0) cc_final: 0.6882 (mm-30) REVERT: B 415 LYS cc_start: 0.7246 (mttt) cc_final: 0.6896 (ttmt) REVERT: B 562 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 602 THR cc_start: 0.9088 (p) cc_final: 0.8572 (t) REVERT: B 607 LEU cc_start: 0.7445 (mt) cc_final: 0.7165 (mt) REVERT: B 620 LYS cc_start: 0.8214 (mttt) cc_final: 0.7171 (pptt) REVERT: B 639 ASP cc_start: 0.7378 (m-30) cc_final: 0.7098 (m-30) REVERT: B 690 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7042 (tttm) REVERT: B 702 ASN cc_start: 0.7919 (t0) cc_final: 0.7527 (t0) REVERT: B 752 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6543 (mt-10) REVERT: B 784 PHE cc_start: 0.7850 (m-10) cc_final: 0.7138 (m-80) REVERT: B 799 TYR cc_start: 0.7882 (t80) cc_final: 0.7549 (t80) REVERT: B 803 GLU cc_start: 0.7048 (tp30) cc_final: 0.6707 (mm-30) REVERT: B 806 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: B 824 LEU cc_start: 0.7792 (mt) cc_final: 0.7565 (tp) REVERT: D 332 MET cc_start: 0.7824 (mmt) cc_final: 0.7413 (mmm) REVERT: D 366 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7346 (mm-30) REVERT: D 376 GLU cc_start: 0.6399 (tp30) cc_final: 0.6034 (tm-30) REVERT: D 380 MET cc_start: 0.6463 (ptp) cc_final: 0.6112 (ptm) REVERT: D 415 LYS cc_start: 0.7143 (mttt) cc_final: 0.6592 (ptpt) REVERT: D 419 GLN cc_start: 0.7490 (mt0) cc_final: 0.7250 (mt0) REVERT: D 422 TYR cc_start: 0.5817 (p90) cc_final: 0.5247 (p90) REVERT: D 562 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7137 (mt-10) REVERT: D 602 THR cc_start: 0.9111 (p) cc_final: 0.8666 (t) REVERT: D 620 LYS cc_start: 0.7990 (mttt) cc_final: 0.7404 (pptt) REVERT: D 639 ASP cc_start: 0.7297 (m-30) cc_final: 0.6815 (m-30) REVERT: D 645 LYS cc_start: 0.7904 (tptp) cc_final: 0.7645 (tptp) REVERT: D 690 LYS cc_start: 0.7867 (mtpt) cc_final: 0.7136 (tttm) REVERT: D 697 SER cc_start: 0.7323 (OUTLIER) cc_final: 0.6685 (p) REVERT: D 702 ASN cc_start: 0.7576 (t0) cc_final: 0.7024 (t0) REVERT: D 761 TYR cc_start: 0.7785 (t80) cc_final: 0.7341 (t80) REVERT: D 784 PHE cc_start: 0.7742 (m-80) cc_final: 0.7046 (m-10) outliers start: 62 outliers final: 35 residues processed: 402 average time/residue: 0.3068 time to fit residues: 184.9361 Evaluate side-chains 369 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 328 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 635 GLN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 817 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 HIS ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 746 HIS ** D 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18320 Z= 0.194 Angle : 0.507 9.680 24788 Z= 0.258 Chirality : 0.039 0.167 2820 Planarity : 0.003 0.035 3212 Dihedral : 6.130 58.880 2524 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.20 % Favored : 93.59 % Rotamer: Outliers : 4.47 % Allowed : 18.04 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2308 helix: 1.20 (0.17), residues: 1012 sheet: -2.06 (0.28), residues: 364 loop : -1.83 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 582 HIS 0.005 0.001 HIS C 657 PHE 0.018 0.001 PHE B 872 TYR 0.010 0.001 TYR B 761 ARG 0.003 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 338 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7814 (mmt) cc_final: 0.7474 (mmm) REVERT: A 363 GLU cc_start: 0.7327 (tp30) cc_final: 0.7117 (mm-30) REVERT: A 365 LYS cc_start: 0.6478 (mmtp) cc_final: 0.6242 (tppt) REVERT: A 366 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 385 ARG cc_start: 0.7483 (ptm160) cc_final: 0.6486 (mmm160) REVERT: A 415 LYS cc_start: 0.7177 (mttt) cc_final: 0.6544 (ptpt) REVERT: A 602 THR cc_start: 0.9058 (p) cc_final: 0.8556 (t) REVERT: A 639 ASP cc_start: 0.7256 (m-30) cc_final: 0.6728 (m-30) REVERT: A 664 LEU cc_start: 0.3752 (OUTLIER) cc_final: 0.3444 (pp) REVERT: A 666 ASN cc_start: 0.6924 (p0) cc_final: 0.6714 (p0) REVERT: A 690 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7069 (tttm) REVERT: A 702 ASN cc_start: 0.7673 (t0) cc_final: 0.7391 (t0) REVERT: A 705 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 712 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7783 (mtm180) REVERT: A 761 TYR cc_start: 0.7705 (t80) cc_final: 0.7290 (t80) REVERT: A 784 PHE cc_start: 0.7922 (m-80) cc_final: 0.7424 (m-80) REVERT: A 806 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7491 (m-10) REVERT: A 845 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7851 (mmtm) REVERT: C 332 MET cc_start: 0.7818 (mmt) cc_final: 0.7480 (mmm) REVERT: C 365 LYS cc_start: 0.6941 (mmtp) cc_final: 0.6469 (tppt) REVERT: C 366 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 385 ARG cc_start: 0.7383 (ptm160) cc_final: 0.6543 (mmm160) REVERT: C 407 ASN cc_start: 0.7410 (m110) cc_final: 0.7030 (m-40) REVERT: C 415 LYS cc_start: 0.7185 (mttt) cc_final: 0.6545 (ptpt) REVERT: C 583 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7782 (mmmt) REVERT: C 639 ASP cc_start: 0.7371 (m-30) cc_final: 0.7098 (m-30) REVERT: C 666 ASN cc_start: 0.7135 (p0) cc_final: 0.6795 (p0) REVERT: C 690 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7094 (tttm) REVERT: C 702 ASN cc_start: 0.7891 (t0) cc_final: 0.7482 (t0) REVERT: C 784 PHE cc_start: 0.7863 (m-80) cc_final: 0.7036 (m-10) REVERT: C 799 TYR cc_start: 0.8130 (t80) cc_final: 0.7831 (t80) REVERT: C 803 GLU cc_start: 0.7061 (tp30) cc_final: 0.6692 (mm-30) REVERT: C 806 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: C 824 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 332 MET cc_start: 0.7940 (mmt) cc_final: 0.7576 (mmm) REVERT: B 365 LYS cc_start: 0.6949 (tppt) cc_final: 0.6658 (tppt) REVERT: B 366 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7288 (mm-30) REVERT: B 385 ARG cc_start: 0.7403 (ptm160) cc_final: 0.6511 (mmm160) REVERT: B 410 GLU cc_start: 0.7168 (tt0) cc_final: 0.6963 (mm-30) REVERT: B 415 LYS cc_start: 0.7210 (mttt) cc_final: 0.6622 (ptpt) REVERT: B 602 THR cc_start: 0.8898 (p) cc_final: 0.8381 (t) REVERT: B 607 LEU cc_start: 0.7542 (mt) cc_final: 0.7267 (mt) REVERT: B 639 ASP cc_start: 0.7345 (m-30) cc_final: 0.7040 (m-30) REVERT: B 690 LYS cc_start: 0.7607 (mtpt) cc_final: 0.7054 (tttm) REVERT: B 702 ASN cc_start: 0.7868 (t0) cc_final: 0.7544 (t0) REVERT: B 784 PHE cc_start: 0.7911 (m-80) cc_final: 0.7238 (m-10) REVERT: B 799 TYR cc_start: 0.7899 (t80) cc_final: 0.7553 (t80) REVERT: B 803 GLU cc_start: 0.7052 (tp30) cc_final: 0.6680 (mm-30) REVERT: B 806 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: B 824 LEU cc_start: 0.7740 (mt) cc_final: 0.7479 (tp) REVERT: D 332 MET cc_start: 0.8023 (mmt) cc_final: 0.7647 (mmm) REVERT: D 363 GLU cc_start: 0.7361 (tp30) cc_final: 0.7118 (mm-30) REVERT: D 366 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7318 (mm-30) REVERT: D 385 ARG cc_start: 0.7405 (ptm160) cc_final: 0.6526 (mmm160) REVERT: D 415 LYS cc_start: 0.7160 (mttt) cc_final: 0.6544 (ptpt) REVERT: D 419 GLN cc_start: 0.7605 (mt0) cc_final: 0.7334 (mt0) REVERT: D 422 TYR cc_start: 0.6001 (p90) cc_final: 0.5334 (p90) REVERT: D 562 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7174 (mt-10) REVERT: D 602 THR cc_start: 0.9123 (p) cc_final: 0.8640 (t) REVERT: D 639 ASP cc_start: 0.7330 (m-30) cc_final: 0.6830 (m-30) REVERT: D 690 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7055 (tttm) REVERT: D 697 SER cc_start: 0.7350 (OUTLIER) cc_final: 0.6814 (p) REVERT: D 702 ASN cc_start: 0.7441 (t0) cc_final: 0.6993 (t0) REVERT: D 761 TYR cc_start: 0.7771 (t80) cc_final: 0.7328 (t80) REVERT: D 784 PHE cc_start: 0.7858 (m-80) cc_final: 0.7124 (m-10) REVERT: D 806 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7315 (m-10) outliers start: 86 outliers final: 61 residues processed: 386 average time/residue: 0.3041 time to fit residues: 179.7304 Evaluate side-chains 394 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 325 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 635 GLN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 810 MET Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 817 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 chunk 55 optimal weight: 7.9990 chunk 224 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 GLN A 657 HIS ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** D 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18320 Z= 0.152 Angle : 0.484 10.313 24788 Z= 0.244 Chirality : 0.038 0.157 2820 Planarity : 0.003 0.031 3212 Dihedral : 5.934 59.747 2524 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.24 % Favored : 94.50 % Rotamer: Outliers : 3.69 % Allowed : 19.39 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2308 helix: 1.33 (0.17), residues: 1012 sheet: -1.62 (0.29), residues: 344 loop : -1.79 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 582 HIS 0.002 0.001 HIS B 751 PHE 0.018 0.001 PHE D 872 TYR 0.009 0.001 TYR B 761 ARG 0.002 0.000 ARG D 554 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 351 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7835 (mmt) cc_final: 0.7478 (mmm) REVERT: A 365 LYS cc_start: 0.6404 (mmtp) cc_final: 0.6166 (tppt) REVERT: A 366 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 385 ARG cc_start: 0.7267 (ptm160) cc_final: 0.6393 (mmm160) REVERT: A 415 LYS cc_start: 0.7110 (mttt) cc_final: 0.6504 (ptpt) REVERT: A 422 TYR cc_start: 0.5845 (p90) cc_final: 0.5439 (p90) REVERT: A 602 THR cc_start: 0.9017 (p) cc_final: 0.8533 (t) REVERT: A 639 ASP cc_start: 0.7235 (m-30) cc_final: 0.6700 (m-30) REVERT: A 664 LEU cc_start: 0.3465 (OUTLIER) cc_final: 0.3212 (pp) REVERT: A 690 LYS cc_start: 0.7628 (mtpt) cc_final: 0.7053 (tttm) REVERT: A 702 ASN cc_start: 0.7636 (t0) cc_final: 0.7367 (t0) REVERT: A 705 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 712 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7759 (mtm180) REVERT: A 761 TYR cc_start: 0.7754 (t80) cc_final: 0.7402 (t80) REVERT: A 784 PHE cc_start: 0.7920 (m-80) cc_final: 0.7485 (m-80) REVERT: A 806 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: A 845 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7798 (mmtm) REVERT: C 332 MET cc_start: 0.7821 (mmt) cc_final: 0.7481 (mmm) REVERT: C 365 LYS cc_start: 0.6935 (mmtp) cc_final: 0.6585 (tppt) REVERT: C 385 ARG cc_start: 0.7386 (ptm160) cc_final: 0.6535 (mmm160) REVERT: C 407 ASN cc_start: 0.7370 (m110) cc_final: 0.6971 (m-40) REVERT: C 415 LYS cc_start: 0.7129 (mttt) cc_final: 0.6473 (ptpt) REVERT: C 583 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7791 (mmmt) REVERT: C 639 ASP cc_start: 0.7304 (m-30) cc_final: 0.6775 (m-30) REVERT: C 666 ASN cc_start: 0.7146 (p0) cc_final: 0.6853 (p0) REVERT: C 673 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7813 (mp0) REVERT: C 690 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7089 (tttm) REVERT: C 702 ASN cc_start: 0.7776 (t0) cc_final: 0.7447 (t0) REVERT: C 784 PHE cc_start: 0.7882 (m-80) cc_final: 0.7163 (m-10) REVERT: C 799 TYR cc_start: 0.7930 (t80) cc_final: 0.7681 (t80) REVERT: C 803 GLU cc_start: 0.7025 (tp30) cc_final: 0.6665 (mm-30) REVERT: C 806 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: C 824 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7699 (mp) REVERT: B 332 MET cc_start: 0.7952 (mmt) cc_final: 0.7571 (mmm) REVERT: B 366 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 376 GLU cc_start: 0.6290 (tp30) cc_final: 0.5751 (tp30) REVERT: B 385 ARG cc_start: 0.7388 (ptm160) cc_final: 0.6521 (mmm160) REVERT: B 415 LYS cc_start: 0.7125 (mttt) cc_final: 0.6524 (ptpt) REVERT: B 602 THR cc_start: 0.8887 (p) cc_final: 0.8388 (t) REVERT: B 607 LEU cc_start: 0.7494 (mt) cc_final: 0.7202 (mt) REVERT: B 639 ASP cc_start: 0.7345 (m-30) cc_final: 0.7040 (m-30) REVERT: B 690 LYS cc_start: 0.7607 (mtpt) cc_final: 0.7050 (tttm) REVERT: B 702 ASN cc_start: 0.7755 (t0) cc_final: 0.7496 (t0) REVERT: B 799 TYR cc_start: 0.7742 (t80) cc_final: 0.7477 (t80) REVERT: B 803 GLU cc_start: 0.7073 (tp30) cc_final: 0.6689 (mm-30) REVERT: B 806 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: B 824 LEU cc_start: 0.7705 (mt) cc_final: 0.7459 (tp) REVERT: D 332 MET cc_start: 0.8040 (mmt) cc_final: 0.7400 (mmm) REVERT: D 363 GLU cc_start: 0.7370 (tp30) cc_final: 0.7154 (mm-30) REVERT: D 366 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7313 (mm-30) REVERT: D 376 GLU cc_start: 0.6367 (tp30) cc_final: 0.6015 (tm-30) REVERT: D 380 MET cc_start: 0.6625 (ptp) cc_final: 0.6352 (ptt) REVERT: D 385 ARG cc_start: 0.7378 (ptm160) cc_final: 0.6385 (mmm160) REVERT: D 415 LYS cc_start: 0.7107 (mttt) cc_final: 0.6469 (ptpt) REVERT: D 419 GLN cc_start: 0.7475 (mt0) cc_final: 0.7193 (mt0) REVERT: D 422 TYR cc_start: 0.6005 (p90) cc_final: 0.5356 (p90) REVERT: D 602 THR cc_start: 0.9062 (p) cc_final: 0.8572 (t) REVERT: D 639 ASP cc_start: 0.7323 (m-30) cc_final: 0.6807 (m-30) REVERT: D 690 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7049 (tttm) REVERT: D 697 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7349 (p) REVERT: D 702 ASN cc_start: 0.7408 (t0) cc_final: 0.6923 (t0) REVERT: D 703 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7520 (mttp) REVERT: D 761 TYR cc_start: 0.7658 (t80) cc_final: 0.7241 (t80) REVERT: D 767 LYS cc_start: 0.7536 (tmtt) cc_final: 0.7176 (ttpp) REVERT: D 784 PHE cc_start: 0.7866 (m-80) cc_final: 0.7144 (m-10) REVERT: D 806 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7254 (m-10) outliers start: 71 outliers final: 55 residues processed: 392 average time/residue: 0.2859 time to fit residues: 172.2475 Evaluate side-chains 394 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 330 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 703 LYS Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 136 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 138 optimal weight: 0.0980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 HIS ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18320 Z= 0.140 Angle : 0.489 10.591 24788 Z= 0.247 Chirality : 0.038 0.173 2820 Planarity : 0.003 0.031 3212 Dihedral : 5.713 55.957 2524 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.37 % Favored : 94.37 % Rotamer: Outliers : 3.79 % Allowed : 20.22 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2308 helix: 1.48 (0.17), residues: 996 sheet: -1.40 (0.29), residues: 344 loop : -1.68 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 582 HIS 0.003 0.001 HIS C 751 PHE 0.020 0.001 PHE D 872 TYR 0.009 0.001 TYR B 761 ARG 0.002 0.000 ARG B 554 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 360 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7831 (mmt) cc_final: 0.7522 (mmm) REVERT: A 365 LYS cc_start: 0.6396 (mmtp) cc_final: 0.6182 (tppt) REVERT: A 366 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7084 (mm-30) REVERT: A 385 ARG cc_start: 0.7276 (ptm160) cc_final: 0.6405 (mmm160) REVERT: A 415 LYS cc_start: 0.7032 (mttt) cc_final: 0.6420 (ptpt) REVERT: A 422 TYR cc_start: 0.5669 (p90) cc_final: 0.5162 (p90) REVERT: A 602 THR cc_start: 0.8996 (p) cc_final: 0.8515 (t) REVERT: A 639 ASP cc_start: 0.7121 (m-30) cc_final: 0.6853 (m-30) REVERT: A 664 LEU cc_start: 0.3470 (OUTLIER) cc_final: 0.3233 (pp) REVERT: A 690 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7056 (tttm) REVERT: A 702 ASN cc_start: 0.7529 (t0) cc_final: 0.7324 (t0) REVERT: A 705 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7543 (mt-10) REVERT: A 712 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7768 (mtm180) REVERT: A 761 TYR cc_start: 0.7732 (t80) cc_final: 0.7460 (t80) REVERT: A 767 LYS cc_start: 0.7033 (tttp) cc_final: 0.6714 (ttpp) REVERT: A 806 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: A 845 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7843 (mptt) REVERT: C 332 MET cc_start: 0.7854 (mmt) cc_final: 0.7548 (mmm) REVERT: C 365 LYS cc_start: 0.6880 (mmtp) cc_final: 0.6618 (tppt) REVERT: C 366 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7169 (mm-30) REVERT: C 385 ARG cc_start: 0.7365 (ptm160) cc_final: 0.6504 (mmm160) REVERT: C 415 LYS cc_start: 0.7130 (mttt) cc_final: 0.6448 (ptpt) REVERT: C 422 TYR cc_start: 0.5639 (p90) cc_final: 0.5207 (p90) REVERT: C 578 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6623 (ttm) REVERT: C 583 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7800 (mmmt) REVERT: C 635 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5250 (tp-100) REVERT: C 639 ASP cc_start: 0.7316 (m-30) cc_final: 0.6780 (m-30) REVERT: C 690 LYS cc_start: 0.7688 (mtpt) cc_final: 0.7064 (tttm) REVERT: C 702 ASN cc_start: 0.7768 (t0) cc_final: 0.7430 (t0) REVERT: C 752 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6426 (mt-10) REVERT: C 784 PHE cc_start: 0.7900 (m-80) cc_final: 0.7212 (m-80) REVERT: C 799 TYR cc_start: 0.7858 (t80) cc_final: 0.7648 (t80) REVERT: C 803 GLU cc_start: 0.7052 (tp30) cc_final: 0.6656 (mm-30) REVERT: C 806 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: C 824 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7709 (mp) REVERT: B 332 MET cc_start: 0.7952 (mmt) cc_final: 0.7570 (mmm) REVERT: B 366 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 385 ARG cc_start: 0.7363 (ptm160) cc_final: 0.6492 (mmm160) REVERT: B 415 LYS cc_start: 0.7064 (mttt) cc_final: 0.6436 (ptpt) REVERT: B 602 THR cc_start: 0.8896 (p) cc_final: 0.8413 (t) REVERT: B 607 LEU cc_start: 0.7385 (mt) cc_final: 0.7170 (mt) REVERT: B 639 ASP cc_start: 0.7350 (m-30) cc_final: 0.6787 (m-30) REVERT: B 690 LYS cc_start: 0.7528 (mtpt) cc_final: 0.6963 (tttm) REVERT: B 702 ASN cc_start: 0.7703 (t0) cc_final: 0.7472 (t0) REVERT: B 784 PHE cc_start: 0.7902 (m-80) cc_final: 0.7436 (m-80) REVERT: B 799 TYR cc_start: 0.7674 (t80) cc_final: 0.7398 (t80) REVERT: B 803 GLU cc_start: 0.7090 (tp30) cc_final: 0.6678 (mm-30) REVERT: B 806 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: B 824 LEU cc_start: 0.7698 (mt) cc_final: 0.7458 (tp) REVERT: D 332 MET cc_start: 0.8056 (mmt) cc_final: 0.7660 (mmm) REVERT: D 363 GLU cc_start: 0.7352 (tp30) cc_final: 0.7139 (mm-30) REVERT: D 366 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7303 (mm-30) REVERT: D 376 GLU cc_start: 0.6337 (tp30) cc_final: 0.5963 (tm-30) REVERT: D 380 MET cc_start: 0.6625 (ptp) cc_final: 0.6316 (ptt) REVERT: D 385 ARG cc_start: 0.7368 (ptm160) cc_final: 0.6347 (mmm160) REVERT: D 415 LYS cc_start: 0.7072 (mttt) cc_final: 0.6434 (ptpt) REVERT: D 419 GLN cc_start: 0.7429 (mt0) cc_final: 0.7151 (mt0) REVERT: D 422 TYR cc_start: 0.5966 (p90) cc_final: 0.5341 (p90) REVERT: D 602 THR cc_start: 0.9033 (p) cc_final: 0.8541 (t) REVERT: D 639 ASP cc_start: 0.7320 (m-30) cc_final: 0.6802 (m-30) REVERT: D 690 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7041 (tttm) REVERT: D 697 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7350 (p) REVERT: D 702 ASN cc_start: 0.7311 (t0) cc_final: 0.6802 (t0) REVERT: D 712 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7458 (mtm180) REVERT: D 761 TYR cc_start: 0.7726 (t80) cc_final: 0.7390 (t80) REVERT: D 767 LYS cc_start: 0.7480 (tmtt) cc_final: 0.7127 (ttpp) REVERT: D 784 PHE cc_start: 0.7794 (m-80) cc_final: 0.7085 (m-10) REVERT: D 806 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7289 (m-10) outliers start: 73 outliers final: 53 residues processed: 399 average time/residue: 0.2935 time to fit residues: 180.1333 Evaluate side-chains 405 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 342 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 635 GLN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 67 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 152 optimal weight: 0.0770 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 GLN A 746 HIS ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 HIS ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 GLN ** D 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18320 Z= 0.173 Angle : 0.506 11.189 24788 Z= 0.256 Chirality : 0.039 0.153 2820 Planarity : 0.003 0.030 3212 Dihedral : 5.637 53.451 2524 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.32 % Rotamer: Outliers : 3.95 % Allowed : 21.10 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2308 helix: 1.44 (0.17), residues: 996 sheet: -1.28 (0.29), residues: 344 loop : -1.63 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 582 HIS 0.003 0.001 HIS C 657 PHE 0.028 0.001 PHE D 872 TYR 0.009 0.001 TYR B 761 ARG 0.003 0.000 ARG D 554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 348 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7610 (mmt) cc_final: 0.7323 (mmm) REVERT: A 365 LYS cc_start: 0.6592 (mmtp) cc_final: 0.6319 (tppt) REVERT: A 366 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 385 ARG cc_start: 0.7267 (ptm160) cc_final: 0.6378 (mmm160) REVERT: A 407 ASN cc_start: 0.7320 (m110) cc_final: 0.6922 (m-40) REVERT: A 415 LYS cc_start: 0.7053 (mttt) cc_final: 0.6418 (ptpt) REVERT: A 422 TYR cc_start: 0.5679 (p90) cc_final: 0.5211 (p90) REVERT: A 602 THR cc_start: 0.9022 (p) cc_final: 0.8528 (t) REVERT: A 639 ASP cc_start: 0.7224 (m-30) cc_final: 0.6948 (m-30) REVERT: A 664 LEU cc_start: 0.3446 (OUTLIER) cc_final: 0.3211 (pp) REVERT: A 690 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7007 (tttm) REVERT: A 702 ASN cc_start: 0.7578 (t0) cc_final: 0.7355 (t0) REVERT: A 705 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7569 (mt-10) REVERT: A 712 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7646 (mtm180) REVERT: A 761 TYR cc_start: 0.7756 (t80) cc_final: 0.7537 (t80) REVERT: A 767 LYS cc_start: 0.7036 (tttp) cc_final: 0.6723 (ttpp) REVERT: A 845 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7852 (mptt) REVERT: C 332 MET cc_start: 0.7853 (mmt) cc_final: 0.7338 (mmm) REVERT: C 365 LYS cc_start: 0.6894 (mmtp) cc_final: 0.6625 (tppt) REVERT: C 366 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7199 (mm-30) REVERT: C 385 ARG cc_start: 0.7400 (ptm160) cc_final: 0.6369 (mmm160) REVERT: C 415 LYS cc_start: 0.7151 (mttt) cc_final: 0.6452 (ptpt) REVERT: C 422 TYR cc_start: 0.5677 (p90) cc_final: 0.5220 (p90) REVERT: C 578 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6751 (ttm) REVERT: C 639 ASP cc_start: 0.7339 (m-30) cc_final: 0.6824 (m-30) REVERT: C 673 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 690 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7024 (tttm) REVERT: C 702 ASN cc_start: 0.7831 (t0) cc_final: 0.7433 (t0) REVERT: C 784 PHE cc_start: 0.7912 (m-80) cc_final: 0.7232 (m-10) REVERT: C 799 TYR cc_start: 0.7903 (t80) cc_final: 0.7670 (t80) REVERT: C 803 GLU cc_start: 0.7105 (tp30) cc_final: 0.6658 (mm-30) REVERT: C 806 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: C 824 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7784 (mp) REVERT: B 332 MET cc_start: 0.7966 (mmt) cc_final: 0.7569 (mmm) REVERT: B 366 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7112 (mm-30) REVERT: B 385 ARG cc_start: 0.7391 (ptm160) cc_final: 0.6354 (mmm160) REVERT: B 415 LYS cc_start: 0.7092 (mttt) cc_final: 0.6433 (ptpt) REVERT: B 602 THR cc_start: 0.8920 (p) cc_final: 0.8448 (t) REVERT: B 639 ASP cc_start: 0.7369 (m-30) cc_final: 0.6802 (m-30) REVERT: B 690 LYS cc_start: 0.7569 (mtpt) cc_final: 0.6993 (tttm) REVERT: B 702 ASN cc_start: 0.7746 (t0) cc_final: 0.7485 (t0) REVERT: B 784 PHE cc_start: 0.7939 (m-80) cc_final: 0.7440 (m-80) REVERT: B 799 TYR cc_start: 0.7717 (t80) cc_final: 0.7474 (t80) REVERT: B 803 GLU cc_start: 0.7162 (tp30) cc_final: 0.6695 (mm-30) REVERT: B 806 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: B 824 LEU cc_start: 0.7744 (mt) cc_final: 0.7497 (tp) REVERT: D 332 MET cc_start: 0.8071 (mmt) cc_final: 0.7662 (mmm) REVERT: D 363 GLU cc_start: 0.7348 (tp30) cc_final: 0.7144 (mm-30) REVERT: D 366 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7289 (mm-30) REVERT: D 376 GLU cc_start: 0.6343 (tp30) cc_final: 0.5821 (tp30) REVERT: D 385 ARG cc_start: 0.7390 (ptm160) cc_final: 0.6396 (mmm160) REVERT: D 415 LYS cc_start: 0.7139 (mttt) cc_final: 0.6467 (ptpt) REVERT: D 419 GLN cc_start: 0.7484 (mt0) cc_final: 0.7211 (mt0) REVERT: D 422 TYR cc_start: 0.5656 (p90) cc_final: 0.5156 (p90) REVERT: D 602 THR cc_start: 0.9049 (p) cc_final: 0.8562 (t) REVERT: D 639 ASP cc_start: 0.7260 (m-30) cc_final: 0.6983 (m-30) REVERT: D 690 LYS cc_start: 0.7756 (mtpt) cc_final: 0.7120 (tttm) REVERT: D 697 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7357 (p) REVERT: D 702 ASN cc_start: 0.7352 (t0) cc_final: 0.6848 (t0) REVERT: D 767 LYS cc_start: 0.7514 (tmtt) cc_final: 0.7167 (ttpp) REVERT: D 784 PHE cc_start: 0.7832 (m-80) cc_final: 0.7095 (m-10) REVERT: D 806 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7336 (m-10) outliers start: 76 outliers final: 62 residues processed: 388 average time/residue: 0.2859 time to fit residues: 170.4034 Evaluate side-chains 401 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 331 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 806 PHE Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18320 Z= 0.202 Angle : 0.526 11.451 24788 Z= 0.267 Chirality : 0.039 0.153 2820 Planarity : 0.003 0.031 3212 Dihedral : 5.638 51.180 2524 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.63 % Favored : 94.15 % Rotamer: Outliers : 4.11 % Allowed : 21.15 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2308 helix: 1.30 (0.17), residues: 1000 sheet: -1.15 (0.29), residues: 344 loop : -1.70 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 582 HIS 0.003 0.001 HIS C 751 PHE 0.021 0.001 PHE D 872 TYR 0.010 0.001 TYR D 761 ARG 0.003 0.000 ARG B 554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 341 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7672 (mmt) cc_final: 0.7382 (mmm) REVERT: A 365 LYS cc_start: 0.6597 (mmtp) cc_final: 0.6326 (tppt) REVERT: A 366 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 385 ARG cc_start: 0.7344 (ptm160) cc_final: 0.6439 (mmm160) REVERT: A 415 LYS cc_start: 0.7133 (mttt) cc_final: 0.6490 (ptpt) REVERT: A 422 TYR cc_start: 0.5684 (p90) cc_final: 0.5166 (p90) REVERT: A 602 THR cc_start: 0.9046 (p) cc_final: 0.8549 (t) REVERT: A 690 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7019 (tttm) REVERT: A 702 ASN cc_start: 0.7628 (t0) cc_final: 0.7416 (t0) REVERT: A 705 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7607 (mt-10) REVERT: A 712 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7670 (mtm180) REVERT: A 761 TYR cc_start: 0.7766 (t80) cc_final: 0.7541 (t80) REVERT: A 767 LYS cc_start: 0.7073 (tttp) cc_final: 0.6764 (ttpp) REVERT: A 806 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: A 845 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7829 (mmtm) REVERT: C 332 MET cc_start: 0.7884 (mmt) cc_final: 0.7453 (mmm) REVERT: C 385 ARG cc_start: 0.7410 (ptm160) cc_final: 0.6364 (mmm160) REVERT: C 415 LYS cc_start: 0.7151 (mttt) cc_final: 0.6457 (ptpt) REVERT: C 422 TYR cc_start: 0.5834 (p90) cc_final: 0.5342 (p90) REVERT: C 639 ASP cc_start: 0.7335 (m-30) cc_final: 0.6785 (m-30) REVERT: C 673 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8242 (mm-30) REVERT: C 690 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7045 (tttm) REVERT: C 702 ASN cc_start: 0.7864 (t0) cc_final: 0.7459 (t0) REVERT: C 784 PHE cc_start: 0.7898 (m-80) cc_final: 0.7187 (m-10) REVERT: C 799 TYR cc_start: 0.7914 (t80) cc_final: 0.7703 (t80) REVERT: C 803 GLU cc_start: 0.7108 (tp30) cc_final: 0.6636 (mm-30) REVERT: C 806 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: C 824 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 332 MET cc_start: 0.7984 (mmt) cc_final: 0.7582 (mmm) REVERT: B 366 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 385 ARG cc_start: 0.7422 (ptm160) cc_final: 0.6392 (mmm160) REVERT: B 415 LYS cc_start: 0.7123 (mttt) cc_final: 0.6442 (ptpt) REVERT: B 602 THR cc_start: 0.8954 (p) cc_final: 0.8476 (t) REVERT: B 639 ASP cc_start: 0.7383 (m-30) cc_final: 0.7078 (m-30) REVERT: B 690 LYS cc_start: 0.7590 (mtpt) cc_final: 0.7012 (tttm) REVERT: B 702 ASN cc_start: 0.7745 (t0) cc_final: 0.7531 (t0) REVERT: B 784 PHE cc_start: 0.7971 (m-80) cc_final: 0.7493 (m-80) REVERT: B 799 TYR cc_start: 0.7766 (t80) cc_final: 0.7501 (t80) REVERT: B 803 GLU cc_start: 0.7131 (tp30) cc_final: 0.6643 (mm-30) REVERT: B 806 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: B 824 LEU cc_start: 0.7798 (mt) cc_final: 0.7524 (tp) REVERT: D 332 MET cc_start: 0.8108 (mmt) cc_final: 0.7456 (mmm) REVERT: D 366 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7283 (mm-30) REVERT: D 385 ARG cc_start: 0.7394 (ptm160) cc_final: 0.6391 (mmm160) REVERT: D 422 TYR cc_start: 0.5795 (p90) cc_final: 0.5270 (p90) REVERT: D 602 THR cc_start: 0.9071 (p) cc_final: 0.8591 (t) REVERT: D 639 ASP cc_start: 0.7252 (m-30) cc_final: 0.6965 (m-30) REVERT: D 690 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7012 (tttm) REVERT: D 696 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5508 (ttm) REVERT: D 697 SER cc_start: 0.7439 (OUTLIER) cc_final: 0.6988 (p) REVERT: D 702 ASN cc_start: 0.7452 (t0) cc_final: 0.6930 (t0) REVERT: D 767 LYS cc_start: 0.7489 (tmtt) cc_final: 0.7084 (ttpp) REVERT: D 784 PHE cc_start: 0.7885 (m-80) cc_final: 0.7190 (m-10) outliers start: 79 outliers final: 68 residues processed: 382 average time/residue: 0.2855 time to fit residues: 167.9222 Evaluate side-chains 402 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 327 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 635 GLN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 696 MET Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 184 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 GLN ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18320 Z= 0.165 Angle : 0.528 11.904 24788 Z= 0.267 Chirality : 0.039 0.153 2820 Planarity : 0.003 0.031 3212 Dihedral : 5.485 46.539 2524 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.72 % Favored : 94.06 % Rotamer: Outliers : 3.53 % Allowed : 21.83 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2308 helix: 1.36 (0.17), residues: 1000 sheet: -1.04 (0.29), residues: 344 loop : -1.64 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 582 HIS 0.003 0.001 HIS C 751 PHE 0.021 0.001 PHE D 872 TYR 0.011 0.001 TYR D 761 ARG 0.003 0.000 ARG B 554 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 337 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.7673 (mmt) cc_final: 0.7384 (mmm) REVERT: A 365 LYS cc_start: 0.6614 (mmtp) cc_final: 0.6347 (tppt) REVERT: A 366 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 385 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6407 (mmm160) REVERT: A 415 LYS cc_start: 0.7130 (mttt) cc_final: 0.6484 (ptpt) REVERT: A 422 TYR cc_start: 0.5663 (p90) cc_final: 0.5157 (p90) REVERT: A 554 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7871 (ttm110) REVERT: A 567 CYS cc_start: 0.8372 (m) cc_final: 0.7837 (m) REVERT: A 602 THR cc_start: 0.9020 (p) cc_final: 0.8529 (t) REVERT: A 690 LYS cc_start: 0.7667 (mtpt) cc_final: 0.6998 (tttm) REVERT: A 702 ASN cc_start: 0.7582 (t0) cc_final: 0.7358 (t0) REVERT: A 705 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7594 (mt-10) REVERT: A 712 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7648 (mtm180) REVERT: A 761 TYR cc_start: 0.7816 (t80) cc_final: 0.7580 (t80) REVERT: A 767 LYS cc_start: 0.7047 (tttp) cc_final: 0.6748 (ttpp) REVERT: A 806 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: A 845 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7806 (mmtm) REVERT: C 332 MET cc_start: 0.7967 (mmt) cc_final: 0.7427 (mmm) REVERT: C 363 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6957 (mm-30) REVERT: C 385 ARG cc_start: 0.7393 (ptm160) cc_final: 0.6330 (mmm160) REVERT: C 415 LYS cc_start: 0.7158 (mttt) cc_final: 0.6422 (ptpt) REVERT: C 422 TYR cc_start: 0.5833 (p90) cc_final: 0.5344 (p90) REVERT: C 639 ASP cc_start: 0.7356 (m-30) cc_final: 0.6820 (m-30) REVERT: C 673 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8266 (mm-30) REVERT: C 690 LYS cc_start: 0.7739 (mtpt) cc_final: 0.7089 (tttm) REVERT: C 702 ASN cc_start: 0.7753 (t0) cc_final: 0.7309 (t0) REVERT: C 784 PHE cc_start: 0.7910 (m-80) cc_final: 0.7279 (m-10) REVERT: C 803 GLU cc_start: 0.7097 (tp30) cc_final: 0.6619 (mm-30) REVERT: C 806 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: C 824 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7849 (mp) REVERT: B 332 MET cc_start: 0.7986 (mmt) cc_final: 0.7586 (mmm) REVERT: B 366 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7123 (mm-30) REVERT: B 385 ARG cc_start: 0.7400 (ptm160) cc_final: 0.6360 (mmm160) REVERT: B 415 LYS cc_start: 0.7133 (mttt) cc_final: 0.6447 (ptpt) REVERT: B 602 THR cc_start: 0.8928 (p) cc_final: 0.8458 (t) REVERT: B 639 ASP cc_start: 0.7378 (m-30) cc_final: 0.6801 (m-30) REVERT: B 690 LYS cc_start: 0.7621 (mtpt) cc_final: 0.7060 (tttm) REVERT: B 784 PHE cc_start: 0.7954 (m-80) cc_final: 0.7485 (m-80) REVERT: B 799 TYR cc_start: 0.7669 (t80) cc_final: 0.7431 (t80) REVERT: B 803 GLU cc_start: 0.7146 (tp30) cc_final: 0.6659 (mm-30) REVERT: B 806 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: B 824 LEU cc_start: 0.7853 (mt) cc_final: 0.7594 (tp) REVERT: D 332 MET cc_start: 0.8090 (mmt) cc_final: 0.7422 (mmm) REVERT: D 366 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7256 (mm-30) REVERT: D 385 ARG cc_start: 0.7378 (ptm160) cc_final: 0.6353 (mmm160) REVERT: D 415 LYS cc_start: 0.7207 (mttt) cc_final: 0.6506 (ptpt) REVERT: D 422 TYR cc_start: 0.5685 (p90) cc_final: 0.5189 (p90) REVERT: D 602 THR cc_start: 0.9046 (p) cc_final: 0.8567 (t) REVERT: D 639 ASP cc_start: 0.7240 (m-30) cc_final: 0.6951 (m-30) REVERT: D 690 LYS cc_start: 0.7727 (mtpt) cc_final: 0.7079 (tttm) REVERT: D 697 SER cc_start: 0.7436 (OUTLIER) cc_final: 0.6985 (p) REVERT: D 702 ASN cc_start: 0.7227 (t0) cc_final: 0.6674 (t0) REVERT: D 767 LYS cc_start: 0.7495 (tmtt) cc_final: 0.7103 (ttpp) REVERT: D 784 PHE cc_start: 0.7797 (m-80) cc_final: 0.7131 (m-10) outliers start: 68 outliers final: 61 residues processed: 375 average time/residue: 0.2912 time to fit residues: 169.0597 Evaluate side-chains 394 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 327 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 806 PHE Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 ASN Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 806 PHE Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 857 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 600 GLN A 635 GLN A 657 HIS ** A 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** B 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN ** D 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.116729 restraints weight = 23959.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120025 restraints weight = 13546.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122126 restraints weight = 9442.673| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18320 Z= 0.280 Angle : 0.581 11.490 24788 Z= 0.295 Chirality : 0.041 0.157 2820 Planarity : 0.003 0.031 3212 Dihedral : 5.684 52.460 2524 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.72 % Favored : 93.07 % Rotamer: Outliers : 4.31 % Allowed : 20.95 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2308 helix: 1.09 (0.17), residues: 1000 sheet: -1.17 (0.34), residues: 256 loop : -1.48 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 582 HIS 0.004 0.001 HIS A 746 PHE 0.021 0.002 PHE D 872 TYR 0.015 0.002 TYR C 799 ARG 0.007 0.001 ARG A 636 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.56 seconds wall clock time: 75 minutes 17.47 seconds (4517.47 seconds total)