Starting phenix.real_space_refine on Thu Sep 18 19:45:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj7_38395/09_2025/8xj7_38395.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj7_38395/09_2025/8xj7_38395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xj7_38395/09_2025/8xj7_38395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj7_38395/09_2025/8xj7_38395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xj7_38395/09_2025/8xj7_38395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj7_38395/09_2025/8xj7_38395.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.128 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: 6 Type Number sf(0) Gaussians P 22 5.49 5 Mg 3 5.21 5 S 94 5.16 5 C 12486 2.51 5 N 3299 2.21 5 O 3691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19595 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3035 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 358} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3601 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3666 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3611 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2934 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 346} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2447 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain breaks: 6 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 3.67, per 1000 atoms: 0.19 Number of scatterers: 19595 At special positions: 0 Unit cell: (115.271, 128.199, 130.353, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 94 16.00 P 22 15.00 Mg 3 11.99 O 3691 8.00 N 3299 7.00 C 12486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.7 microseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4630 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 33 sheets defined 43.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.544A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 376 through 381 removed outlier: 4.038A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.833A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.922A pdb=" N GLU A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.730A pdb=" N CYS A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.700A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.524A pdb=" N TYR A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 removed outlier: 4.565A pdb=" N TYR A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.503A pdb=" N LEU B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.825A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.826A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.897A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 579 removed outlier: 4.043A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.830A pdb=" N ASN B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.566A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 695 No H-bonds generated for 'chain 'B' and resid 693 through 695' Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.501A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 719 removed outlier: 4.236A pdb=" N THR B 718 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 744 Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.929A pdb=" N PHE B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.610A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 381 removed outlier: 4.011A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.798A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.788A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN C 463 " --> pdb=" O GLU C 459 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN C 466 " --> pdb=" O MET C 462 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 571 through 577 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 654 through 661 removed outlier: 3.535A pdb=" N LYS C 658 " --> pdb=" O GLY C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 696 through 705 Processing helix chain 'C' and resid 710 through 714 removed outlier: 3.550A pdb=" N HIS C 713 " --> pdb=" O SER C 710 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 714 " --> pdb=" O VAL C 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 710 through 714' Processing helix chain 'C' and resid 716 through 723 removed outlier: 4.405A pdb=" N LYS C 722 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 723 " --> pdb=" O ASP C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 744 Processing helix chain 'C' and resid 748 through 764 removed outlier: 7.386A pdb=" N HIS C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.530A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 454 through 469 removed outlier: 4.226A pdb=" N MET D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.878A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.544A pdb=" N ASP D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.841A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 659 Processing helix chain 'D' and resid 666 through 680 Processing helix chain 'D' and resid 693 through 695 No H-bonds generated for 'chain 'D' and resid 693 through 695' Processing helix chain 'D' and resid 696 through 704 Processing helix chain 'D' and resid 716 through 722 removed outlier: 4.529A pdb=" N LYS D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 745 removed outlier: 3.513A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 Processing helix chain 'D' and resid 758 through 763 Processing helix chain 'E' and resid 325 through 335 Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 372 through 375 removed outlier: 3.932A pdb=" N LEU E 375 " --> pdb=" O ARG E 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.896A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 430 through 436 removed outlier: 3.983A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E 436 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 469 removed outlier: 4.170A pdb=" N MET E 458 " --> pdb=" O ASP E 454 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 488 Processing helix chain 'E' and resid 509 through 521 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 570 through 577 removed outlier: 3.623A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 641 removed outlier: 3.704A pdb=" N GLU E 640 " --> pdb=" O ARG E 636 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN E 641 " --> pdb=" O GLU E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 659 Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'E' and resid 695 through 704 removed outlier: 4.470A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 704 " --> pdb=" O LEU E 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'F' and resid 362 through 372 removed outlier: 3.946A pdb=" N LYS F 366 " --> pdb=" O PRO F 362 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.683A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 430 through 434 Processing helix chain 'F' and resid 454 through 469 removed outlier: 4.662A pdb=" N MET F 458 " --> pdb=" O ASP F 454 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE F 468 " --> pdb=" O ILE F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 488 Processing helix chain 'F' and resid 509 through 521 Processing helix chain 'F' and resid 544 through 548 removed outlier: 3.541A pdb=" N HIS F 548 " --> pdb=" O ALA F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 579 removed outlier: 3.748A pdb=" N THR F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU F 579 " --> pdb=" O LYS F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 Processing helix chain 'F' and resid 654 through 659 Processing helix chain 'F' and resid 664 through 680 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 415 removed outlier: 3.534A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.224A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.572A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA7, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AA8, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.347A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.276A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 706 through 707 Processing sheet with id=AB3, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB4, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB5, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.295A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB7, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.548A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AB9, first strand: chain 'C' and resid 726 through 728 removed outlier: 3.756A pdb=" N ILE C 726 " --> pdb=" O THR C 733 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC2, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC3, first strand: chain 'D' and resid 524 through 527 removed outlier: 4.374A pdb=" N SER D 556 " --> pdb=" O THR D 527 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC5, first strand: chain 'D' and resid 629 through 631 removed outlier: 6.575A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AC7, first strand: chain 'D' and resid 726 through 728 Processing sheet with id=AC8, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC9, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.780A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET E 426 " --> pdb=" O ASP E 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 524 through 527 removed outlier: 6.846A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 628 through 631 Processing sheet with id=AD3, first strand: chain 'F' and resid 339 through 341 removed outlier: 4.321A pdb=" N HIS F 347 " --> pdb=" O ASN F 358 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.849A pdb=" N GLY F 418 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 524 through 527 removed outlier: 6.322A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR F 499 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 628 through 631 659 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3194 1.30 - 1.43: 5063 1.43 - 1.56: 11577 1.56 - 1.69: 38 1.69 - 1.81: 141 Bond restraints: 20013 Sorted by residual: bond pdb=" O3A ANP C 801 " pdb=" PB ANP C 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" O3A ANP E 801 " pdb=" PB ANP E 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" O3A ANP D 801 " pdb=" PB ANP D 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.06e+01 ... (remaining 20008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 26948 3.59 - 7.18: 147 7.18 - 10.77: 21 10.77 - 14.36: 6 14.36 - 17.95: 4 Bond angle restraints: 27126 Sorted by residual: angle pdb=" PB ANP C 801 " pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 126.95 109.00 17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.17 17.78 3.00e+00 1.11e-01 3.51e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.19 17.76 3.00e+00 1.11e-01 3.50e+01 angle pdb=" PB ANP D 801 " pdb=" N3B ANP D 801 " pdb=" PG ANP D 801 " ideal model delta sigma weight residual 126.95 109.65 17.30 3.00e+00 1.11e-01 3.32e+01 angle pdb=" C SER B 708 " pdb=" N SER B 709 " pdb=" CA SER B 709 " ideal model delta sigma weight residual 121.90 115.35 6.55 1.26e+00 6.30e-01 2.71e+01 ... (remaining 27121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 11111 22.98 - 45.96: 858 45.96 - 68.94: 173 68.94 - 91.92: 63 91.92 - 114.90: 5 Dihedral angle restraints: 12210 sinusoidal: 5089 harmonic: 7121 Sorted by residual: dihedral pdb=" CA VAL D 707 " pdb=" C VAL D 707 " pdb=" N SER D 708 " pdb=" CA SER D 708 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL B 707 " pdb=" C VAL B 707 " pdb=" N SER B 708 " pdb=" CA SER B 708 " ideal model delta harmonic sigma weight residual 180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA MET C 462 " pdb=" C MET C 462 " pdb=" N ASN C 463 " pdb=" CA ASN C 463 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 12207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2546 0.054 - 0.108: 477 0.108 - 0.162: 44 0.162 - 0.217: 0 0.217 - 0.271: 8 Chirality restraints: 3075 Sorted by residual: chirality pdb=" CB ILE A 569 " pdb=" CA ILE A 569 " pdb=" CG1 ILE A 569 " pdb=" CG2 ILE A 569 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ANP F 801 " pdb=" C2' ANP F 801 " pdb=" C4' ANP F 801 " pdb=" O3' ANP F 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ANP E 801 " pdb=" C2' ANP E 801 " pdb=" C4' ANP E 801 " pdb=" O3' ANP E 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3072 not shown) Planarity restraints: 3398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 689 " -0.079 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO F 690 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO F 690 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 690 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 758 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C SER D 758 " 0.066 2.00e-02 2.50e+03 pdb=" O SER D 758 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE D 759 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 455 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C SER C 455 " -0.041 2.00e-02 2.50e+03 pdb=" O SER C 455 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO C 456 " 0.014 2.00e-02 2.50e+03 ... (remaining 3395 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 209 2.60 - 3.18: 16132 3.18 - 3.75: 29663 3.75 - 4.33: 44011 4.33 - 4.90: 70879 Nonbonded interactions: 160894 Sorted by model distance: nonbonded pdb=" OG SER C 510 " pdb="MG MG C 802 " model vdw 2.027 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A 802 " model vdw 2.070 2.170 nonbonded pdb=" OG SER B 510 " pdb="MG MG B 802 " model vdw 2.090 2.170 nonbonded pdb=" OE2 GLU C 653 " pdb=" OH TYR D 687 " model vdw 2.209 3.040 nonbonded pdb=" N GLU A 474 " pdb=" OE1 GLU A 474 " model vdw 2.220 3.120 ... (remaining 160889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 324 through 359 or (resid 360 through 361 and (name N or n \ ame CA or name C or name O or name CB )) or resid 362 through 533 or (resid 534 \ and (name N or name CA or name C or name O or name CB )) or resid 542 through 56 \ 3 or resid 567 through 583 or resid 594 through 652 or (resid 653 and (name N or \ name CA or name C or name O or name CB )) or resid 654 through 691 or (resid 69 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 693 through \ 700)) selection = (chain 'E' and (resid 324 through 642 or (resid 643 through 644 and (name N or n \ ame CA or name C or name O or name CB )) or resid 645 through 697 or (resid 698 \ and (name N or name CA or name C or name O or name CB )) or resid 699 or (resid \ 700 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 324 through 635 or (resid 636 through 639 and (name N or n \ ame CA or name C or name O or name CB )) or resid 640 through 642 or (resid 643 \ through 644 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 5 through 715 or (resid 716 and (name N or name CA or name C or name O or name C \ B )) or resid 717 through 718 or (resid 719 through 720 and (name N or name CA o \ r name C or name O or name CB )) or resid 721 through 728 or (resid 729 through \ 730 and (name N or name CA or name C or name O or name CB )) or resid 731 throug \ h 763 or (resid 764 and (name N or name CA or name C or name O or name CB )) or \ resid 773 through 779 or (resid 780 and (name N or name CA or name C or name O o \ r name CB )) or resid 781 through 801)) selection = (chain 'C' and (resid 324 through 635 or (resid 636 through 639 and (name N or n \ ame CA or name C or name O or name CB )) or resid 640 through 642 or (resid 643 \ through 644 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 5 through 708 or (resid 709 through 710 and (name N or name CA or name C or name \ O or name CB )) or resid 711 through 715 or (resid 716 and (name N or name CA o \ r name C or name O or name CB )) or resid 717 through 718 or (resid 719 through \ 720 and (name N or name CA or name C or name O or name CB )) or resid 721 or (re \ sid 722 through 723 and (name N or name CA or name C or name O or name CB )) or \ resid 724 through 727 or (resid 728 through 730 and (name N or name CA or name C \ or name O or name CB )) or resid 731 through 735 or (resid 736 and (name N or n \ ame CA or name C or name O or name CB )) or resid 737 through 740 or (resid 741 \ through 742 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 3 through 744 or (resid 745 and (name N or name CA or name C or name O or name C \ B )) or resid 746 through 750 or (resid 751 and (name N or name CA or name C or \ name O or name CB )) or resid 752 through 756 or (resid 757 and (name N or name \ CA or name C or name O or name CB )) or resid 758 through 763 or (resid 764 and \ (name N or name CA or name C or name O or name CB )) or (resid 773 and (name N o \ r name CA or name C or name O or name CB )) or resid 774 through 801)) selection = (chain 'D' and (resid 324 through 708 or (resid 709 through 710 and (name N or n \ ame CA or name C or name O or name CB )) or resid 711 through 722 or (resid 723 \ and (name N or name CA or name C or name O or name CB )) or resid 724 through 72 \ 7 or (resid 728 through 730 and (name N or name CA or name C or name O or name C \ B )) or resid 731 through 735 or (resid 736 and (name N or name CA or name C or \ name O or name CB )) or resid 737 through 750 or (resid 751 and (name N or name \ CA or name C or name O or name CB )) or resid 752 through 756 or (resid 757 and \ (name N or name CA or name C or name O or name CB )) or resid 758 through 761 or \ (resid 762 and (name N or name CA or name C or name O or name CB )) or resid 76 \ 3 through 764 or (resid 773 and (name N or name CA or name C or name O or name C \ B )) or resid 774 through 779 or (resid 780 and (name N or name CA or name C or \ name O or name CB )) or resid 781 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.100 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: 0.040 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.820 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.005 0.143 20013 Z= 0.229 Angle : 0.729 17.951 27126 Z= 0.350 Chirality : 0.043 0.271 3075 Planarity : 0.005 0.118 3398 Dihedral : 17.625 114.902 7580 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.08 % Favored : 94.63 % Rotamer: Outliers : 1.55 % Allowed : 17.85 % Favored : 80.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.17), residues: 2384 helix: 0.11 (0.18), residues: 857 sheet: 0.00 (0.32), residues: 289 loop : -0.87 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 387 TYR 0.017 0.001 TYR C 482 PHE 0.032 0.001 PHE C 698 TRP 0.021 0.001 TRP F 675 HIS 0.004 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00465 (20013) covalent geometry : angle 0.72861 (27126) hydrogen bonds : bond 0.19508 ( 659) hydrogen bonds : angle 7.18105 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.660 Fit side-chains REVERT: C 537 ASP cc_start: 0.7772 (p0) cc_final: 0.7274 (p0) REVERT: E 576 LYS cc_start: 0.8312 (tttt) cc_final: 0.7722 (tmmt) outliers start: 33 outliers final: 25 residues processed: 262 average time/residue: 0.5873 time to fit residues: 173.5878 Evaluate side-chains 256 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 626 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.0000 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 0.0670 overall best weight: 0.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN C 593 ASN F 597 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116911 restraints weight = 23783.647| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.13 r_work: 0.3264 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20013 Z= 0.102 Angle : 0.540 8.198 27126 Z= 0.280 Chirality : 0.041 0.176 3075 Planarity : 0.004 0.074 3398 Dihedral : 12.050 142.632 2887 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.99 % Favored : 94.71 % Rotamer: Outliers : 2.34 % Allowed : 15.32 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.17), residues: 2384 helix: 0.39 (0.18), residues: 880 sheet: -0.20 (0.32), residues: 301 loop : -0.85 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 387 TYR 0.015 0.001 TYR C 482 PHE 0.021 0.001 PHE C 698 TRP 0.010 0.001 TRP F 675 HIS 0.004 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00225 (20013) covalent geometry : angle 0.53979 (27126) hydrogen bonds : bond 0.03426 ( 659) hydrogen bonds : angle 5.07215 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 0.801 Fit side-chains REVERT: A 332 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8417 (mtt90) REVERT: A 450 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7224 (mptp) REVERT: A 618 MET cc_start: 0.7118 (mmm) cc_final: 0.6312 (tmm) REVERT: A 684 MET cc_start: 0.7939 (tmm) cc_final: 0.7580 (tpt) REVERT: B 332 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8202 (mtt-85) REVERT: B 387 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7882 (mpp-170) REVERT: B 557 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6758 (mm-30) REVERT: B 618 MET cc_start: 0.8997 (mtm) cc_final: 0.8782 (mtm) REVERT: C 390 LYS cc_start: 0.8612 (mttt) cc_final: 0.8335 (mppt) REVERT: C 537 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7065 (p0) REVERT: C 547 MET cc_start: 0.8740 (mtp) cc_final: 0.8497 (mtp) REVERT: D 775 GLN cc_start: 0.7193 (pm20) cc_final: 0.6949 (pt0) REVERT: E 426 MET cc_start: 0.7148 (ttm) cc_final: 0.6936 (tpp) REVERT: E 461 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8226 (tm) REVERT: F 387 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7636 (mtm180) REVERT: F 551 ARG cc_start: 0.7618 (mmt90) cc_final: 0.7333 (mmt90) REVERT: F 664 TYR cc_start: 0.5595 (m-80) cc_final: 0.5146 (m-80) outliers start: 50 outliers final: 16 residues processed: 305 average time/residue: 0.6856 time to fit residues: 233.2716 Evaluate side-chains 269 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 0.4980 chunk 186 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 228 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN A 642 ASN B 529 GLN B 660 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.170940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112441 restraints weight = 23037.376| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.24 r_work: 0.3100 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20013 Z= 0.158 Angle : 0.569 9.041 27126 Z= 0.297 Chirality : 0.043 0.171 3075 Planarity : 0.004 0.057 3398 Dihedral : 10.954 141.799 2859 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.29 % Favored : 94.42 % Rotamer: Outliers : 3.51 % Allowed : 15.97 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.17), residues: 2384 helix: 0.46 (0.18), residues: 872 sheet: -0.24 (0.32), residues: 291 loop : -0.87 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 663 TYR 0.022 0.001 TYR B 482 PHE 0.015 0.002 PHE D 524 TRP 0.015 0.001 TRP F 675 HIS 0.009 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00384 (20013) covalent geometry : angle 0.56857 (27126) hydrogen bonds : bond 0.03785 ( 659) hydrogen bonds : angle 4.85063 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 266 time to evaluate : 0.644 Fit side-chains REVERT: A 375 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 387 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7692 (mtt90) REVERT: A 575 LYS cc_start: 0.8735 (ttmt) cc_final: 0.7913 (mppt) REVERT: A 618 MET cc_start: 0.7256 (mmm) cc_final: 0.6493 (tmm) REVERT: B 387 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7891 (mpp80) REVERT: B 653 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: C 537 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7245 (p0) REVERT: D 757 GLU cc_start: 0.7385 (mp0) cc_final: 0.7151 (mp0) REVERT: D 775 GLN cc_start: 0.7107 (pm20) cc_final: 0.6798 (pt0) REVERT: E 426 MET cc_start: 0.7317 (ttm) cc_final: 0.7069 (tpp) REVERT: E 461 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (tm) REVERT: F 486 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6452 (mm) REVERT: F 551 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7442 (mmt90) REVERT: F 664 TYR cc_start: 0.5643 (m-80) cc_final: 0.5291 (m-80) outliers start: 75 outliers final: 40 residues processed: 314 average time/residue: 0.6119 time to fit residues: 215.7122 Evaluate side-chains 287 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 ASN B 529 GLN B 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.173638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116563 restraints weight = 23861.318| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.38 r_work: 0.3228 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20013 Z= 0.111 Angle : 0.526 9.344 27126 Z= 0.277 Chirality : 0.042 0.291 3075 Planarity : 0.004 0.049 3398 Dihedral : 10.512 141.682 2859 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.95 % Favored : 94.76 % Rotamer: Outliers : 3.04 % Allowed : 17.33 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.17), residues: 2384 helix: 0.64 (0.18), residues: 873 sheet: -0.28 (0.31), residues: 297 loop : -0.83 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 387 TYR 0.017 0.001 TYR B 482 PHE 0.024 0.001 PHE C 698 TRP 0.014 0.001 TRP F 675 HIS 0.006 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00261 (20013) covalent geometry : angle 0.52561 (27126) hydrogen bonds : bond 0.02924 ( 659) hydrogen bonds : angle 4.57151 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 268 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 387 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7676 (mtt90) REVERT: A 575 LYS cc_start: 0.8689 (ttmt) cc_final: 0.7842 (mppt) REVERT: A 618 MET cc_start: 0.7181 (mmm) cc_final: 0.6473 (tmm) REVERT: B 387 ARG cc_start: 0.8255 (ttm110) cc_final: 0.7778 (mpp80) REVERT: C 537 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7099 (p0) REVERT: D 775 GLN cc_start: 0.7005 (pm20) cc_final: 0.6573 (pt0) REVERT: D 780 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6456 (pp20) REVERT: E 390 LYS cc_start: 0.8672 (mmpt) cc_final: 0.8174 (mtmt) REVERT: E 426 MET cc_start: 0.7145 (ttm) cc_final: 0.6921 (tpp) REVERT: E 461 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8259 (tm) REVERT: F 351 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6829 (mt) REVERT: F 387 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7561 (mtm180) REVERT: F 486 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6306 (mm) REVERT: F 664 TYR cc_start: 0.5701 (m-80) cc_final: 0.5395 (m-80) outliers start: 65 outliers final: 28 residues processed: 308 average time/residue: 0.6613 time to fit residues: 228.8386 Evaluate side-chains 279 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 50 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 203 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN B 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.170193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121982 restraints weight = 22891.838| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.50 r_work: 0.3029 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20013 Z= 0.156 Angle : 0.563 10.531 27126 Z= 0.294 Chirality : 0.043 0.214 3075 Planarity : 0.004 0.059 3398 Dihedral : 10.577 143.724 2859 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.33 % Favored : 94.38 % Rotamer: Outliers : 3.75 % Allowed : 17.66 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.17), residues: 2384 helix: 0.61 (0.18), residues: 877 sheet: -0.37 (0.31), residues: 297 loop : -0.86 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 387 TYR 0.022 0.001 TYR B 482 PHE 0.014 0.002 PHE D 524 TRP 0.018 0.001 TRP F 675 HIS 0.009 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00379 (20013) covalent geometry : angle 0.56316 (27126) hydrogen bonds : bond 0.03430 ( 659) hydrogen bonds : angle 4.58046 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 249 time to evaluate : 0.833 Fit side-chains REVERT: A 375 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8268 (mt) REVERT: A 387 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7541 (mtt90) REVERT: A 575 LYS cc_start: 0.8779 (ttmt) cc_final: 0.7963 (mppt) REVERT: A 618 MET cc_start: 0.7148 (mmm) cc_final: 0.6584 (tmm) REVERT: B 387 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7967 (mpp80) REVERT: C 537 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7309 (p0) REVERT: D 775 GLN cc_start: 0.6985 (pm20) cc_final: 0.6619 (pt0) REVERT: D 780 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6503 (pp20) REVERT: E 461 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8352 (tm) REVERT: F 351 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6930 (mt) REVERT: F 486 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6420 (mm) REVERT: F 532 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6155 (tt) REVERT: F 551 ARG cc_start: 0.7658 (mmt90) cc_final: 0.7364 (mmt90) REVERT: F 569 ILE cc_start: 0.6647 (OUTLIER) cc_final: 0.6404 (mp) REVERT: F 664 TYR cc_start: 0.5989 (m-80) cc_final: 0.5677 (m-80) outliers start: 80 outliers final: 46 residues processed: 302 average time/residue: 0.6061 time to fit residues: 206.9717 Evaluate side-chains 290 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 0.0270 chunk 220 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN B 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.172902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127586 restraints weight = 22853.432| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.78 r_work: 0.3095 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20013 Z= 0.097 Angle : 0.512 10.502 27126 Z= 0.269 Chirality : 0.041 0.181 3075 Planarity : 0.004 0.056 3398 Dihedral : 10.250 142.631 2857 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.99 % Favored : 94.71 % Rotamer: Outliers : 2.72 % Allowed : 18.97 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.17), residues: 2384 helix: 0.84 (0.18), residues: 872 sheet: -0.30 (0.31), residues: 297 loop : -0.77 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 387 TYR 0.016 0.001 TYR C 482 PHE 0.027 0.001 PHE C 698 TRP 0.017 0.001 TRP F 675 HIS 0.004 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00222 (20013) covalent geometry : angle 0.51187 (27126) hydrogen bonds : bond 0.02656 ( 659) hydrogen bonds : angle 4.37567 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 0.761 Fit side-chains REVERT: A 387 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7531 (mtt90) REVERT: A 450 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7461 (mptp) REVERT: A 575 LYS cc_start: 0.8773 (ttmt) cc_final: 0.7953 (mppt) REVERT: A 618 MET cc_start: 0.7310 (mmm) cc_final: 0.6725 (tmm) REVERT: B 504 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: C 537 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7182 (p0) REVERT: D 557 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6924 (pp20) REVERT: D 775 GLN cc_start: 0.6914 (pm20) cc_final: 0.6586 (pt0) REVERT: E 481 LEU cc_start: 0.8226 (tp) cc_final: 0.7971 (tp) REVERT: F 387 ARG cc_start: 0.8332 (mtp180) cc_final: 0.7695 (mtm180) REVERT: F 532 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6181 (tt) REVERT: F 551 ARG cc_start: 0.7615 (mmt90) cc_final: 0.7406 (mmt90) REVERT: F 664 TYR cc_start: 0.6045 (m-80) cc_final: 0.5721 (m-80) outliers start: 58 outliers final: 29 residues processed: 300 average time/residue: 0.6662 time to fit residues: 224.7134 Evaluate side-chains 275 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 217 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN B 660 GLN ** E 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126172 restraints weight = 22978.848| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.98 r_work: 0.3091 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20013 Z= 0.098 Angle : 0.522 11.607 27126 Z= 0.272 Chirality : 0.041 0.159 3075 Planarity : 0.004 0.052 3398 Dihedral : 10.133 142.283 2857 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.99 % Favored : 94.71 % Rotamer: Outliers : 2.67 % Allowed : 18.92 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.17), residues: 2384 helix: 0.87 (0.18), residues: 885 sheet: -0.28 (0.31), residues: 293 loop : -0.74 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 387 TYR 0.016 0.001 TYR C 482 PHE 0.013 0.001 PHE B 357 TRP 0.022 0.001 TRP F 675 HIS 0.004 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00229 (20013) covalent geometry : angle 0.52194 (27126) hydrogen bonds : bond 0.02610 ( 659) hydrogen bonds : angle 4.31650 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9042 (tt) cc_final: 0.8742 (tt) REVERT: A 375 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8136 (mt) REVERT: A 387 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7576 (mtt90) REVERT: A 450 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7331 (mptp) REVERT: A 575 LYS cc_start: 0.8753 (ttmt) cc_final: 0.7882 (mppt) REVERT: A 618 MET cc_start: 0.7185 (mmm) cc_final: 0.6635 (tmm) REVERT: B 504 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: B 717 MET cc_start: 0.3674 (ttt) cc_final: 0.3021 (ttm) REVERT: C 537 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7164 (p0) REVERT: C 557 GLU cc_start: 0.6913 (mm-30) cc_final: 0.5113 (mp0) REVERT: D 557 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6874 (pp20) REVERT: D 775 GLN cc_start: 0.6909 (pm20) cc_final: 0.6595 (pt0) REVERT: E 390 LYS cc_start: 0.8564 (mmpt) cc_final: 0.8183 (mtmt) REVERT: E 481 LEU cc_start: 0.8138 (tp) cc_final: 0.7912 (tp) REVERT: E 576 LYS cc_start: 0.8261 (tttt) cc_final: 0.7750 (tmmt) REVERT: F 351 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6803 (mt) REVERT: F 387 ARG cc_start: 0.8280 (mtp180) cc_final: 0.7623 (mtm180) REVERT: F 532 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6267 (tt) REVERT: F 551 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7365 (mmt90) outliers start: 57 outliers final: 32 residues processed: 296 average time/residue: 0.6479 time to fit residues: 216.4396 Evaluate side-chains 275 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 621 ILE Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 220 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN B 660 GLN ** E 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114120 restraints weight = 23110.049| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.20 r_work: 0.3143 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20013 Z= 0.107 Angle : 0.530 12.220 27126 Z= 0.276 Chirality : 0.041 0.153 3075 Planarity : 0.004 0.050 3398 Dihedral : 10.120 142.281 2857 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.95 % Favored : 94.76 % Rotamer: Outliers : 2.53 % Allowed : 19.39 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.17), residues: 2384 helix: 0.92 (0.18), residues: 885 sheet: -0.28 (0.31), residues: 295 loop : -0.73 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 387 TYR 0.017 0.001 TYR B 482 PHE 0.029 0.001 PHE C 698 TRP 0.023 0.001 TRP F 675 HIS 0.005 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00254 (20013) covalent geometry : angle 0.53006 (27126) hydrogen bonds : bond 0.02731 ( 659) hydrogen bonds : angle 4.31111 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 245 time to evaluate : 0.789 Fit side-chains REVERT: A 371 ILE cc_start: 0.9166 (tt) cc_final: 0.8875 (tt) REVERT: A 375 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8131 (mt) REVERT: A 387 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7809 (mtt90) REVERT: A 450 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7326 (mptp) REVERT: A 575 LYS cc_start: 0.8748 (ttmt) cc_final: 0.7845 (mppt) REVERT: A 618 MET cc_start: 0.7317 (mmm) cc_final: 0.6724 (tmm) REVERT: B 504 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: B 717 MET cc_start: 0.3556 (ttt) cc_final: 0.2910 (ttm) REVERT: C 537 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7128 (p0) REVERT: C 557 GLU cc_start: 0.6973 (mm-30) cc_final: 0.5898 (pm20) REVERT: D 557 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6963 (pp20) REVERT: D 649 LYS cc_start: 0.8283 (mptt) cc_final: 0.7958 (mmtm) REVERT: E 390 LYS cc_start: 0.8698 (mmpt) cc_final: 0.8273 (mtmt) REVERT: E 481 LEU cc_start: 0.8131 (tp) cc_final: 0.7905 (tp) REVERT: E 576 LYS cc_start: 0.8251 (tttt) cc_final: 0.7721 (tmmt) REVERT: F 351 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6810 (mt) REVERT: F 387 ARG cc_start: 0.8364 (mtp180) cc_final: 0.7669 (mtm180) REVERT: F 532 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6267 (tt) REVERT: F 551 ARG cc_start: 0.7597 (mmt90) cc_final: 0.7395 (mmt90) REVERT: F 626 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.5079 (m-10) outliers start: 54 outliers final: 36 residues processed: 282 average time/residue: 0.6198 time to fit residues: 198.0244 Evaluate side-chains 277 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 621 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 133 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN B 660 GLN ** E 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.171808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125071 restraints weight = 22863.376| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.92 r_work: 0.3052 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20013 Z= 0.126 Angle : 0.552 11.524 27126 Z= 0.286 Chirality : 0.042 0.150 3075 Planarity : 0.004 0.056 3398 Dihedral : 10.196 142.712 2857 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.16 % Favored : 94.55 % Rotamer: Outliers : 2.58 % Allowed : 19.30 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.17), residues: 2384 helix: 0.86 (0.18), residues: 885 sheet: -0.30 (0.31), residues: 295 loop : -0.73 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 387 TYR 0.019 0.001 TYR B 482 PHE 0.013 0.001 PHE B 357 TRP 0.029 0.001 TRP F 675 HIS 0.006 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00304 (20013) covalent geometry : angle 0.55249 (27126) hydrogen bonds : bond 0.02946 ( 659) hydrogen bonds : angle 4.35494 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 387 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7715 (mtt90) REVERT: A 390 LYS cc_start: 0.8878 (mmpt) cc_final: 0.8542 (mppt) REVERT: A 575 LYS cc_start: 0.8774 (ttmt) cc_final: 0.7921 (mppt) REVERT: A 618 MET cc_start: 0.7285 (mmm) cc_final: 0.6775 (tmm) REVERT: A 684 MET cc_start: 0.8065 (tmm) cc_final: 0.7601 (tpt) REVERT: B 717 MET cc_start: 0.3536 (ttt) cc_final: 0.2895 (ttm) REVERT: C 537 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7239 (p0) REVERT: C 557 GLU cc_start: 0.6856 (mm-30) cc_final: 0.5981 (pm20) REVERT: D 557 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6850 (pp20) REVERT: D 775 GLN cc_start: 0.7077 (pm20) cc_final: 0.6382 (pt0) REVERT: E 390 LYS cc_start: 0.8644 (mmpt) cc_final: 0.8260 (mtmt) REVERT: E 576 LYS cc_start: 0.8272 (tttt) cc_final: 0.7757 (tmmt) REVERT: F 351 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6830 (mt) REVERT: F 387 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7676 (mtm180) REVERT: F 532 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6300 (tt) REVERT: F 626 PHE cc_start: 0.5707 (OUTLIER) cc_final: 0.5089 (m-10) outliers start: 55 outliers final: 40 residues processed: 281 average time/residue: 0.6056 time to fit residues: 193.1424 Evaluate side-chains 278 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 201 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN B 632 GLN B 660 GLN ** E 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123531 restraints weight = 23029.473| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.95 r_work: 0.3028 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20013 Z= 0.160 Angle : 0.587 11.967 27126 Z= 0.303 Chirality : 0.043 0.159 3075 Planarity : 0.004 0.063 3398 Dihedral : 10.364 143.822 2857 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.24 % Favored : 94.46 % Rotamer: Outliers : 2.48 % Allowed : 19.95 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2384 helix: 0.77 (0.18), residues: 877 sheet: -0.30 (0.31), residues: 289 loop : -0.75 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 387 TYR 0.021 0.001 TYR B 482 PHE 0.029 0.002 PHE C 698 TRP 0.038 0.002 TRP F 675 HIS 0.009 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00392 (20013) covalent geometry : angle 0.58742 (27126) hydrogen bonds : bond 0.03298 ( 659) hydrogen bonds : angle 4.45384 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 0.715 Fit side-chains REVERT: A 375 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 387 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7716 (mtt90) REVERT: A 575 LYS cc_start: 0.8789 (ttmt) cc_final: 0.7918 (mppt) REVERT: A 618 MET cc_start: 0.7272 (mmm) cc_final: 0.6787 (tmm) REVERT: A 684 MET cc_start: 0.8106 (tmm) cc_final: 0.7625 (tpt) REVERT: C 405 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: C 537 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7254 (p0) REVERT: C 557 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6083 (pm20) REVERT: D 557 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6842 (pp20) REVERT: D 775 GLN cc_start: 0.7106 (pm20) cc_final: 0.6360 (pt0) REVERT: E 390 LYS cc_start: 0.8689 (mmpt) cc_final: 0.8297 (mtmt) REVERT: E 576 LYS cc_start: 0.8285 (tttt) cc_final: 0.7774 (tmmt) REVERT: F 351 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6903 (mt) REVERT: F 387 ARG cc_start: 0.8286 (mtp180) cc_final: 0.7622 (mtm180) REVERT: F 532 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6303 (tt) REVERT: F 551 ARG cc_start: 0.7476 (mmt90) cc_final: 0.7207 (mmt90) REVERT: F 626 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.5122 (m-10) outliers start: 53 outliers final: 40 residues processed: 281 average time/residue: 0.5863 time to fit residues: 185.7580 Evaluate side-chains 283 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 181 optimal weight: 0.9990 chunk 224 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 529 GLN B 660 GLN ** E 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.170827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124334 restraints weight = 22965.809| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.98 r_work: 0.3037 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20013 Z= 0.135 Angle : 0.563 11.451 27126 Z= 0.292 Chirality : 0.042 0.155 3075 Planarity : 0.004 0.062 3398 Dihedral : 10.315 144.178 2857 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.24 % Favored : 94.46 % Rotamer: Outliers : 2.53 % Allowed : 20.00 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2384 helix: 0.78 (0.18), residues: 878 sheet: -0.27 (0.32), residues: 289 loop : -0.74 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 387 TYR 0.019 0.001 TYR B 482 PHE 0.016 0.001 PHE C 752 TRP 0.038 0.001 TRP F 675 HIS 0.007 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00329 (20013) covalent geometry : angle 0.56266 (27126) hydrogen bonds : bond 0.03038 ( 659) hydrogen bonds : angle 4.41586 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7330.28 seconds wall clock time: 125 minutes 31.42 seconds (7531.42 seconds total)