Starting phenix.real_space_refine on Mon Jul 22 20:01:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/07_2024/8xj7_38395_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/07_2024/8xj7_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/07_2024/8xj7_38395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/07_2024/8xj7_38395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/07_2024/8xj7_38395_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/07_2024/8xj7_38395_neut.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "E GLU 480": "OE1" <-> "OE2" Residue "F GLU 557": "OE1" <-> "OE2" Residue "F GLU 691": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: {'PHE:plan': 1, 'ASP: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, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG: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: {'GLU:plan': 2, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} 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: 10.98, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.35 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 2.60 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: 5.92 Time building geometry restraints manager: 8.02 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: 99.49 - 106.39: 576 106.39 - 113.29: 10924 113.29 - 120.19: 7132 120.19 - 127.09: 8285 127.09 - 133.99: 209 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 2.440 nonbonded pdb=" N GLU A 474 " pdb=" OE1 GLU A 474 " model vdw 2.220 2.520 ... (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 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 782 or resid 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 782 or resid 80 \ 1)) 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 782 or resid 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: 1.150 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.750 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.490 ------------------------------------------------------------------------------- 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= 0.292 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (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 TRP 0.021 0.001 TRP F 675 HIS 0.004 0.001 HIS B 597 PHE 0.032 0.001 PHE C 698 TYR 0.017 0.001 TYR C 482 ARG 0.013 0.000 ARG D 387 *********************** 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 fitting. rotamer outliers: 33 poor density : 236 time to evaluate : 2.336 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: 1.2348 time to fit residues: 366.4583 Evaluate side-chains 256 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 202 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20013 Z= 0.304 Angle : 0.603 7.522 27126 Z= 0.311 Chirality : 0.044 0.175 3075 Planarity : 0.005 0.072 3398 Dihedral : 12.520 140.665 2887 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.45 % Favored : 94.25 % Rotamer: Outliers : 3.56 % Allowed : 16.53 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2384 helix: 0.18 (0.18), residues: 870 sheet: -0.24 (0.30), residues: 325 loop : -0.99 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 675 HIS 0.010 0.001 HIS B 597 PHE 0.018 0.002 PHE C 698 TYR 0.023 0.001 TYR B 482 ARG 0.006 0.000 ARG A 344 *********************** 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 330 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 254 time to evaluate : 2.327 Fit side-chains REVERT: A 361 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: A 513 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8774 (ttpt) REVERT: A 618 MET cc_start: 0.7047 (mmm) cc_final: 0.6370 (tmm) REVERT: B 332 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8076 (mmm-85) REVERT: B 343 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: B 361 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: B 504 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: C 537 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7290 (p0) REVERT: E 458 MET cc_start: 0.8042 (ttp) cc_final: 0.7764 (ttp) REVERT: E 461 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8017 (tm) REVERT: E 462 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7189 (mpp) REVERT: E 663 ARG cc_start: 0.6210 (ttt-90) cc_final: 0.5963 (tpt-90) REVERT: F 486 LEU cc_start: 0.6840 (mt) cc_final: 0.6325 (mm) REVERT: F 664 TYR cc_start: 0.5559 (m-80) cc_final: 0.5133 (m-80) outliers start: 76 outliers final: 36 residues processed: 309 average time/residue: 1.3153 time to fit residues: 459.5308 Evaluate side-chains 282 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 LYS 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 B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 448 ASP 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 555 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 490 LEU 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 603 ASP Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 235 optimal weight: 30.0000 chunk 194 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN B 660 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 594 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20013 Z= 0.420 Angle : 0.655 8.196 27126 Z= 0.340 Chirality : 0.047 0.186 3075 Planarity : 0.005 0.053 3398 Dihedral : 11.470 140.422 2865 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.21 % Favored : 93.50 % Rotamer: Outliers : 5.20 % Allowed : 16.58 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2384 helix: 0.03 (0.17), residues: 875 sheet: -0.33 (0.30), residues: 313 loop : -1.15 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 675 HIS 0.016 0.002 HIS B 597 PHE 0.021 0.002 PHE D 524 TYR 0.025 0.002 TYR B 482 ARG 0.007 0.001 ARG A 387 *********************** 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 360 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 249 time to evaluate : 2.396 Fit side-chains REVERT: A 513 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8753 (ttpt) REVERT: A 618 MET cc_start: 0.7154 (mmm) cc_final: 0.6489 (tmm) REVERT: A 684 MET cc_start: 0.7828 (tmm) cc_final: 0.7559 (tpt) REVERT: B 343 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: B 504 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: B 653 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: C 405 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: C 537 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7509 (p0) REVERT: D 649 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7882 (mptm) REVERT: D 780 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6741 (pp20) REVERT: E 458 MET cc_start: 0.8079 (ttp) cc_final: 0.7679 (ttp) REVERT: E 462 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7059 (mpp) REVERT: F 351 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.6989 (mt) REVERT: F 486 LEU cc_start: 0.7014 (mt) cc_final: 0.6494 (mm) REVERT: F 664 TYR cc_start: 0.5774 (m-80) cc_final: 0.5446 (m-80) outliers start: 111 outliers final: 61 residues processed: 333 average time/residue: 1.2299 time to fit residues: 463.5956 Evaluate side-chains 309 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 239 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 535 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 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 653 GLU 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 452 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain D residue 334 LEU 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 432 ASP Chi-restraints excluded: chain D residue 448 ASP 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 555 CYS 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 432 ASP Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 490 LEU 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 610 PHE Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 366 LYS 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 215 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 219 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN B 660 GLN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20013 Z= 0.210 Angle : 0.541 7.593 27126 Z= 0.285 Chirality : 0.042 0.172 3075 Planarity : 0.004 0.050 3398 Dihedral : 10.747 143.341 2865 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.54 % Favored : 94.17 % Rotamer: Outliers : 3.89 % Allowed : 18.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2384 helix: 0.39 (0.18), residues: 875 sheet: -0.27 (0.30), residues: 319 loop : -1.04 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 675 HIS 0.005 0.001 HIS B 597 PHE 0.024 0.002 PHE C 698 TYR 0.019 0.001 TYR B 482 ARG 0.007 0.000 ARG A 387 *********************** 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 331 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 248 time to evaluate : 2.358 Fit side-chains REVERT: A 618 MET cc_start: 0.7141 (mmm) cc_final: 0.6614 (tmm) REVERT: A 684 MET cc_start: 0.7812 (tmm) cc_final: 0.7572 (tpt) REVERT: B 343 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: C 537 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7306 (p0) REVERT: D 382 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: D 717 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6445 (mmm) REVERT: D 780 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6712 (pp20) REVERT: E 390 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8374 (mtmt) REVERT: F 351 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6847 (mt) REVERT: F 387 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7789 (mtm180) REVERT: F 486 LEU cc_start: 0.7071 (mt) cc_final: 0.6718 (mm) REVERT: F 664 TYR cc_start: 0.5911 (m-80) cc_final: 0.5603 (m-80) outliers start: 83 outliers final: 46 residues processed: 307 average time/residue: 1.2924 time to fit residues: 447.8466 Evaluate side-chains 285 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 232 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 507 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 343 GLU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 507 THR 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 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 C residue 457 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 404 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 641 ASN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 655 LEU 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 193 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 F 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1404 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= 0.211 Angle : 0.546 10.882 27126 Z= 0.285 Chirality : 0.042 0.302 3075 Planarity : 0.004 0.066 3398 Dihedral : 10.569 142.307 2861 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.49 % Favored : 94.21 % Rotamer: Outliers : 4.17 % Allowed : 19.25 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2384 helix: 0.52 (0.18), residues: 877 sheet: -0.20 (0.31), residues: 317 loop : -0.99 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 675 HIS 0.006 0.001 HIS B 597 PHE 0.013 0.001 PHE D 451 TYR 0.020 0.001 TYR B 482 ARG 0.007 0.000 ARG A 387 *********************** 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 331 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 242 time to evaluate : 2.518 Fit side-chains REVERT: A 618 MET cc_start: 0.7143 (mmm) cc_final: 0.6645 (tmm) REVERT: A 684 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7588 (tpt) REVERT: B 343 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: C 537 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7415 (p0) REVERT: D 717 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6491 (mmm) REVERT: E 390 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8370 (mtmt) REVERT: F 351 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6916 (mt) REVERT: F 387 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7782 (mtm180) REVERT: F 486 LEU cc_start: 0.6954 (mt) cc_final: 0.6653 (mm) REVERT: F 664 TYR cc_start: 0.5911 (m-80) cc_final: 0.5576 (m-80) REVERT: F 683 ILE cc_start: 0.7137 (mm) cc_final: 0.6876 (tp) outliers start: 89 outliers final: 57 residues processed: 307 average time/residue: 1.2326 time to fit residues: 428.5528 Evaluate side-chains 293 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 230 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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 432 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 535 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 A residue 684 MET Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 351 ILE 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 507 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 604 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 C residue 455 SER Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 614 ASP 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 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 717 MET 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 390 LYS Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 432 ASP 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 E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 655 LEU 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 78 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 192 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 F 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1510 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= 0.153 Angle : 0.517 9.947 27126 Z= 0.271 Chirality : 0.041 0.250 3075 Planarity : 0.004 0.058 3398 Dihedral : 10.302 142.408 2861 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.29 % Favored : 94.42 % Rotamer: Outliers : 3.70 % Allowed : 19.81 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2384 helix: 0.71 (0.18), residues: 885 sheet: -0.21 (0.31), residues: 313 loop : -0.93 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 675 HIS 0.004 0.001 HIS D 713 PHE 0.028 0.001 PHE C 698 TYR 0.017 0.001 TYR C 482 ARG 0.008 0.000 ARG D 387 *********************** 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 333 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 254 time to evaluate : 2.180 Fit side-chains REVERT: A 618 MET cc_start: 0.7122 (mmm) cc_final: 0.6639 (tmm) REVERT: A 684 MET cc_start: 0.7779 (tmm) cc_final: 0.7543 (tpt) REVERT: A 690 PRO cc_start: 0.7575 (Cg_endo) cc_final: 0.7178 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: B 504 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: C 495 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8171 (mptt) REVERT: C 537 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7290 (p0) REVERT: C 557 GLU cc_start: 0.6862 (mm-30) cc_final: 0.5142 (mp0) REVERT: D 382 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: D 775 GLN cc_start: 0.7046 (pm20) cc_final: 0.6673 (pt0) REVERT: E 390 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8354 (mtmt) REVERT: E 576 LYS cc_start: 0.8365 (tttt) cc_final: 0.7863 (tmmt) REVERT: E 663 ARG cc_start: 0.6347 (ttt-90) cc_final: 0.5961 (tpt-90) REVERT: F 351 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6800 (mt) REVERT: F 387 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7736 (mtm180) outliers start: 79 outliers final: 45 residues processed: 312 average time/residue: 1.1978 time to fit residues: 424.1375 Evaluate side-chains 283 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 231 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 535 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 343 GLU 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 507 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 604 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 C residue 455 SER Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 432 ASP 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 D residue 665 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 432 ASP 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 578 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 655 LEU 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 223 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 F 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20013 Z= 0.189 Angle : 0.538 10.974 27126 Z= 0.280 Chirality : 0.042 0.222 3075 Planarity : 0.004 0.054 3398 Dihedral : 10.281 142.111 2858 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.45 % Favored : 94.25 % Rotamer: Outliers : 3.51 % Allowed : 20.23 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2384 helix: 0.71 (0.18), residues: 891 sheet: -0.18 (0.31), residues: 311 loop : -0.92 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 675 HIS 0.006 0.001 HIS F 548 PHE 0.013 0.001 PHE B 357 TYR 0.019 0.001 TYR B 482 ARG 0.009 0.000 ARG A 387 *********************** 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 315 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 240 time to evaluate : 2.361 Fit side-chains REVERT: A 618 MET cc_start: 0.7131 (mmm) cc_final: 0.6653 (tmm) REVERT: A 684 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7581 (tpt) REVERT: A 690 PRO cc_start: 0.7705 (Cg_endo) cc_final: 0.7331 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: B 504 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: C 495 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8206 (mmtp) REVERT: C 537 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7354 (p0) REVERT: C 557 GLU cc_start: 0.6870 (mm-30) cc_final: 0.5156 (mp0) REVERT: C 731 VAL cc_start: 0.5339 (OUTLIER) cc_final: 0.5002 (p) REVERT: D 382 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: D 717 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6827 (mmm) REVERT: D 775 GLN cc_start: 0.6942 (pm20) cc_final: 0.6568 (pt0) REVERT: E 390 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8369 (mtmt) REVERT: E 576 LYS cc_start: 0.8371 (tttt) cc_final: 0.7898 (tmmt) REVERT: E 663 ARG cc_start: 0.6446 (ttt-90) cc_final: 0.6039 (tpt-90) REVERT: F 351 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6880 (mt) outliers start: 75 outliers final: 50 residues processed: 293 average time/residue: 1.2544 time to fit residues: 416.6603 Evaluate side-chains 292 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 2.483 ------------------------------------------------------------------------------- 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 530 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 351 ILE 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 507 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 455 SER Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 731 VAL 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 382 GLU Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 477 LYS 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 578 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 691 GLU 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 366 LYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 655 LEU 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 143 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 181 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 F 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20013 Z= 0.177 Angle : 0.537 11.682 27126 Z= 0.278 Chirality : 0.042 0.201 3075 Planarity : 0.004 0.051 3398 Dihedral : 10.220 142.332 2858 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.33 % Favored : 94.38 % Rotamer: Outliers : 3.37 % Allowed : 20.47 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2384 helix: 0.70 (0.18), residues: 897 sheet: -0.17 (0.31), residues: 309 loop : -0.95 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 675 HIS 0.009 0.001 HIS F 548 PHE 0.030 0.001 PHE C 698 TYR 0.017 0.001 TYR B 482 ARG 0.010 0.000 ARG D 387 *********************** 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 311 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 239 time to evaluate : 2.257 Fit side-chains REVERT: A 618 MET cc_start: 0.7096 (mmm) cc_final: 0.6648 (tmm) REVERT: A 684 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7571 (tpt) REVERT: A 690 PRO cc_start: 0.7715 (Cg_endo) cc_final: 0.7308 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: B 504 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: C 495 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8200 (mmtm) REVERT: C 537 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7286 (p0) REVERT: C 557 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6237 (tm-30) REVERT: C 731 VAL cc_start: 0.5278 (OUTLIER) cc_final: 0.4892 (p) REVERT: D 382 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: D 717 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6827 (mmm) REVERT: E 390 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8366 (mtmt) REVERT: E 522 ASP cc_start: 0.7710 (m-30) cc_final: 0.7235 (m-30) REVERT: E 529 GLN cc_start: 0.5976 (mp10) cc_final: 0.5665 (mp10) REVERT: E 576 LYS cc_start: 0.8312 (tttt) cc_final: 0.7842 (tmmt) REVERT: E 663 ARG cc_start: 0.6480 (ttt-90) cc_final: 0.6080 (tpt-90) REVERT: F 351 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6840 (mt) outliers start: 72 outliers final: 48 residues processed: 292 average time/residue: 1.2478 time to fit residues: 412.2433 Evaluate side-chains 288 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 2.145 ------------------------------------------------------------------------------- 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 432 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 343 GLU 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 507 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 455 SER Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 731 VAL 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 382 GLU Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP 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 D residue 665 ARG Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 432 ASP 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 E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 214 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 D 763 HIS F 680 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20013 Z= 0.368 Angle : 0.630 10.711 27126 Z= 0.324 Chirality : 0.046 0.238 3075 Planarity : 0.005 0.067 3398 Dihedral : 10.629 139.984 2858 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.91 % Favored : 93.79 % Rotamer: Outliers : 3.89 % Allowed : 20.23 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2384 helix: 0.38 (0.18), residues: 900 sheet: -0.15 (0.31), residues: 310 loop : -1.01 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 675 HIS 0.011 0.001 HIS B 597 PHE 0.022 0.002 PHE D 524 TYR 0.024 0.001 TYR B 482 ARG 0.011 0.001 ARG D 387 *********************** 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 319 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 236 time to evaluate : 2.350 Fit side-chains REVERT: A 332 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.8050 (mtp85) REVERT: A 690 PRO cc_start: 0.7728 (Cg_endo) cc_final: 0.7411 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: B 504 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7230 (mm-30) REVERT: C 495 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8588 (mptt) REVERT: C 537 ASP cc_start: 0.8063 (p0) cc_final: 0.7417 (p0) REVERT: C 557 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6684 (mm-30) REVERT: C 731 VAL cc_start: 0.5097 (OUTLIER) cc_final: 0.4711 (p) REVERT: D 382 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: D 665 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7892 (ttp-170) REVERT: D 717 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6508 (mmm) REVERT: E 576 LYS cc_start: 0.8361 (tttt) cc_final: 0.7870 (tmmt) REVERT: F 351 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.6987 (mt) outliers start: 83 outliers final: 52 residues processed: 300 average time/residue: 1.2585 time to fit residues: 426.9566 Evaluate side-chains 290 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 230 time to evaluate : 2.210 ------------------------------------------------------------------------------- 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 530 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 343 GLU 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 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 581 CYS 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 457 GLU Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 717 MET 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 402 ASP Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 477 LYS 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 578 THR Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 655 LEU 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 141 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 F 680 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20013 Z= 0.170 Angle : 0.547 10.557 27126 Z= 0.283 Chirality : 0.042 0.189 3075 Planarity : 0.004 0.053 3398 Dihedral : 10.278 143.361 2858 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.29 % Favored : 94.42 % Rotamer: Outliers : 3.04 % Allowed : 21.22 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2384 helix: 0.64 (0.18), residues: 897 sheet: -0.17 (0.32), residues: 298 loop : -0.96 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 675 HIS 0.008 0.001 HIS F 548 PHE 0.014 0.001 PHE B 357 TYR 0.017 0.001 TYR C 482 ARG 0.011 0.000 ARG D 387 ********************** 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 299 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 234 time to evaluate : 2.302 Fit side-chains REVERT: A 332 ARG cc_start: 0.8319 (mtt-85) cc_final: 0.8035 (mtp85) REVERT: A 690 PRO cc_start: 0.7666 (Cg_endo) cc_final: 0.7360 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: B 504 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: C 495 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8183 (mmtm) REVERT: C 537 ASP cc_start: 0.7843 (p0) cc_final: 0.7342 (p0) REVERT: C 557 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6591 (mm-30) REVERT: C 731 VAL cc_start: 0.5149 (OUTLIER) cc_final: 0.4799 (p) REVERT: D 382 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: D 717 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6497 (mmm) REVERT: E 576 LYS cc_start: 0.8340 (tttt) cc_final: 0.7857 (tmmt) REVERT: F 351 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6789 (mt) REVERT: F 558 LEU cc_start: 0.7017 (mt) cc_final: 0.6551 (pp) REVERT: F 619 ARG cc_start: 0.7914 (mmt-90) cc_final: 0.7514 (mpp-170) outliers start: 65 outliers final: 46 residues processed: 284 average time/residue: 1.2429 time to fit residues: 399.4767 Evaluate side-chains 290 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 343 GLU 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 507 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 455 SER Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 532 LEU 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 578 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 605 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111210 restraints weight = 22864.532| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.99 r_work: 0.3103 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20013 Z= 0.221 Angle : 0.566 10.898 27126 Z= 0.292 Chirality : 0.043 0.185 3075 Planarity : 0.004 0.061 3398 Dihedral : 10.310 142.108 2858 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.45 % Favored : 94.25 % Rotamer: Outliers : 2.90 % Allowed : 21.64 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2384 helix: 0.63 (0.18), residues: 900 sheet: -0.12 (0.31), residues: 310 loop : -0.91 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 675 HIS 0.007 0.001 HIS F 548 PHE 0.028 0.002 PHE C 698 TYR 0.020 0.001 TYR B 482 ARG 0.011 0.000 ARG D 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7391.01 seconds wall clock time: 130 minutes 2.90 seconds (7802.90 seconds total)