Starting phenix.real_space_refine (version: dev) on Mon Feb 27 01:53:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqk_26697/02_2023/7uqk_26697_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqk_26697/02_2023/7uqk_26697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqk_26697/02_2023/7uqk_26697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqk_26697/02_2023/7uqk_26697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqk_26697/02_2023/7uqk_26697_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqk_26697/02_2023/7uqk_26697_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A ARG 813": "NH1" <-> "NH2" Residue "A ARG 829": "NH1" <-> "NH2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A ARG 929": "NH1" <-> "NH2" Residue "A GLU 1320": "OE1" <-> "OE2" Residue "A GLU 1348": "OE1" <-> "OE2" Residue "A GLU 1373": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 720": "NH1" <-> "NH2" Residue "B GLU 732": "OE1" <-> "OE2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B ARG 812": "NH1" <-> "NH2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B ARG 828": "NH1" <-> "NH2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B GLU 879": "OE1" <-> "OE2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B ARG 928": "NH1" <-> "NH2" Residue "B GLU 935": "OE1" <-> "OE2" Residue "B GLU 1347": "OE1" <-> "OE2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 720": "NH1" <-> "NH2" Residue "C GLU 732": "OE1" <-> "OE2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "C GLU 764": "OE1" <-> "OE2" Residue "C GLU 794": "OE1" <-> "OE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 809": "OE1" <-> "OE2" Residue "C GLU 815": "OE1" <-> "OE2" Residue "C GLU 824": "OE1" <-> "OE2" Residue "C ARG 828": "NH1" <-> "NH2" Residue "C GLU 864": "OE1" <-> "OE2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C GLU 879": "OE1" <-> "OE2" Residue "C GLU 903": "OE1" <-> "OE2" Residue "C GLU 1319": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ARG 448": "NH1" <-> "NH2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D GLU 519": "OE1" <-> "OE2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D GLU 690": "OE1" <-> "OE2" Residue "D ARG 720": "NH1" <-> "NH2" Residue "D GLU 795": "OE1" <-> "OE2" Residue "D GLU 824": "OE1" <-> "OE2" Residue "D ARG 828": "NH1" <-> "NH2" Residue "D GLU 1347": "OE1" <-> "OE2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E ARG 498": "NH1" <-> "NH2" Residue "E GLU 505": "OE1" <-> "OE2" Residue "E GLU 506": "OE1" <-> "OE2" Residue "E PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 720": "NH1" <-> "NH2" Residue "E GLU 794": "OE1" <-> "OE2" Residue "E ARG 812": "NH1" <-> "NH2" Residue "E GLU 815": "OE1" <-> "OE2" Residue "E ARG 828": "NH1" <-> "NH2" Residue "E GLU 873": "OE1" <-> "OE2" Residue "E GLU 879": "OE1" <-> "OE2" Residue "E GLU 903": "OE1" <-> "OE2" Residue "E ARG 928": "NH1" <-> "NH2" Residue "E GLU 1372": "OE1" <-> "OE2" Residue "F GLU 437": "OE1" <-> "OE2" Residue "F ARG 476": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F ARG 498": "NH1" <-> "NH2" Residue "F GLU 505": "OE1" <-> "OE2" Residue "F GLU 506": "OE1" <-> "OE2" Residue "F GLU 519": "OE1" <-> "OE2" Residue "F ARG 572": "NH1" <-> "NH2" Residue "F ARG 573": "NH1" <-> "NH2" Residue "F ARG 720": "NH1" <-> "NH2" Residue "F GLU 732": "OE1" <-> "OE2" Residue "F GLU 733": "OE1" <-> "OE2" Residue "F GLU 760": "OE1" <-> "OE2" Residue "F GLU 795": "OE1" <-> "OE2" Residue "F GLU 809": "OE1" <-> "OE2" Residue "F ARG 812": "NH1" <-> "NH2" Residue "F GLU 815": "OE1" <-> "OE2" Residue "F GLU 824": "OE1" <-> "OE2" Residue "F ARG 828": "NH1" <-> "NH2" Residue "F GLU 873": "OE1" <-> "OE2" Residue "F GLU 879": "OE1" <-> "OE2" Residue "F ARG 928": "NH1" <-> "NH2" Residue "F GLU 1325": "OE1" <-> "OE2" Residue "F GLU 1347": "OE1" <-> "OE2" Residue "F GLU 1372": "OE1" <-> "OE2" Residue "G ARG 323": "NH1" <-> "NH2" Residue "G GLU 957": "OE1" <-> "OE2" Residue "G GLU 1012": "OE1" <-> "OE2" Residue "G PHE 1041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1047": "OD1" <-> "OD2" Residue "G GLU 1051": "OE1" <-> "OE2" Residue "G GLU 1069": "OE1" <-> "OE2" Residue "G GLU 1100": "OE1" <-> "OE2" Residue "G GLU 1119": "OE1" <-> "OE2" Residue "G GLU 1128": "OE1" <-> "OE2" Residue "G GLU 1129": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29142 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4591 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 32, 'TRANS': 543} Chain breaks: 2 Chain: "B" Number of atoms: 4614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4614 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 32, 'TRANS': 546} Chain breaks: 2 Chain: "C" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4607 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 32, 'TRANS': 545} Chain breaks: 2 Chain: "D" Number of atoms: 4586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4586 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 32, 'TRANS': 543} Chain breaks: 2 Chain: "E" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4448 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 32, 'TRANS': 525} Chain breaks: 4 Chain: "F" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4519 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 32, 'TRANS': 534} Chain breaks: 3 Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1642 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.25, per 1000 atoms: 0.56 Number of scatterers: 29142 At special positions: 0 Unit cell: (143.244, 147.384, 158.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 10 15.00 O 5419 8.00 N 4953 7.00 C 18652 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: 10.70 Conformation dependent library (CDL) restraints added in 3.9 seconds 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 166 helices and 13 sheets defined 44.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 438 through 441 No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 535 through 546 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 624 through 642 Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.711A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 648 " --> pdb=" O GLN A 645 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 644 through 648' Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.909A pdb=" N LEU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 672 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 710 removed outlier: 4.902A pdb=" N ALA A 698 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP A 699 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN A 700 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 702 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 703 " --> pdb=" O GLN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 755 through 764 removed outlier: 4.414A pdb=" N PHE A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.883A pdb=" N ALA A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 807 No H-bonds generated for 'chain 'A' and resid 804 through 807' Processing helix chain 'A' and resid 815 through 828 Processing helix chain 'A' and resid 839 through 842 No H-bonds generated for 'chain 'A' and resid 839 through 842' Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.943A pdb=" N LYS A 882 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 889 removed outlier: 4.420A pdb=" N ASP A 888 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 889 " --> pdb=" O LEU A 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 889' Processing helix chain 'A' and resid 903 through 911 removed outlier: 3.580A pdb=" N ARG A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 917 No H-bonds generated for 'chain 'A' and resid 914 through 917' Processing helix chain 'A' and resid 1325 through 1338 Processing helix chain 'A' and resid 1344 through 1360 removed outlier: 3.783A pdb=" N ILE A1357 " --> pdb=" O SER A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1377 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.844A pdb=" N ASP B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 436 through 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.897A pdb=" N LEU B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 523 No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 533 through 546 removed outlier: 4.678A pdb=" N ILE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 598 Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 623 through 641 Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.537A pdb=" N LEU B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 671 " --> pdb=" O MET B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 710 removed outlier: 3.877A pdb=" N LEU B 696 " --> pdb=" O LYS B 693 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA B 697 " --> pdb=" O PRO B 694 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP B 698 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B 700 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN B 701 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN B 702 " --> pdb=" O GLN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 753 through 766 removed outlier: 5.835A pdb=" N PHE B 758 " --> pdb=" O ARG B 754 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 792 removed outlier: 3.932A pdb=" N ALA B 787 " --> pdb=" O GLN B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 808 Processing helix chain 'B' and resid 814 through 826 Processing helix chain 'B' and resid 838 through 844 removed outlier: 3.819A pdb=" N ASN B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 858 removed outlier: 3.547A pdb=" N LEU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 881 Processing helix chain 'B' and resid 886 through 888 No H-bonds generated for 'chain 'B' and resid 886 through 888' Processing helix chain 'B' and resid 902 through 916 Processing helix chain 'B' and resid 1324 through 1337 Processing helix chain 'B' and resid 1343 through 1359 removed outlier: 3.707A pdb=" N ILE B1356 " --> pdb=" O SER B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1367 through 1376 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 419 through 434 Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.703A pdb=" N TYR C 439 " --> pdb=" O PRO C 436 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN C 441 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 520 through 523 No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 534 through 546 Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 588 through 598 removed outlier: 3.538A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 617 Processing helix chain 'C' and resid 623 through 641 Processing helix chain 'C' and resid 643 through 646 Processing helix chain 'C' and resid 663 through 669 Processing helix chain 'C' and resid 692 through 709 removed outlier: 3.895A pdb=" N LEU C 696 " --> pdb=" O LYS C 693 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA C 697 " --> pdb=" O PRO C 694 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASP C 698 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 700 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN C 701 " --> pdb=" O ASP C 698 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN C 702 " --> pdb=" O GLN C 699 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS C 706 " --> pdb=" O LEU C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 754 through 766 removed outlier: 4.409A pdb=" N GLN C 766 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 792 removed outlier: 3.679A pdb=" N ALA C 787 " --> pdb=" O GLN C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 806 No H-bonds generated for 'chain 'C' and resid 803 through 806' Processing helix chain 'C' and resid 814 through 827 Processing helix chain 'C' and resid 838 through 844 removed outlier: 4.205A pdb=" N ASN C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 858 Processing helix chain 'C' and resid 877 through 881 Processing helix chain 'C' and resid 884 through 887 removed outlier: 4.295A pdb=" N ASP C 887 " --> pdb=" O ILE C 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 884 through 887' Processing helix chain 'C' and resid 902 through 916 removed outlier: 4.143A pdb=" N LEU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1324 through 1337 Processing helix chain 'C' and resid 1343 through 1359 removed outlier: 3.814A pdb=" N ILE C1356 " --> pdb=" O SER C1352 " (cutoff:3.500A) Processing helix chain 'C' and resid 1367 through 1376 Processing helix chain 'D' and resid 419 through 429 removed outlier: 4.105A pdb=" N ASP D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET D 428 " --> pdb=" O GLN D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 439 No H-bonds generated for 'chain 'D' and resid 436 through 439' Processing helix chain 'D' and resid 461 through 468 Processing helix chain 'D' and resid 495 through 507 removed outlier: 3.723A pdb=" N LEU D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 522 No H-bonds generated for 'chain 'D' and resid 520 through 522' Processing helix chain 'D' and resid 533 through 542 removed outlier: 4.491A pdb=" N SER D 537 " --> pdb=" O GLN D 533 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.545A pdb=" N THR D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 617 removed outlier: 3.649A pdb=" N LYS D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 641 Processing helix chain 'D' and resid 663 through 672 removed outlier: 4.407A pdb=" N LEU D 668 " --> pdb=" O SER D 664 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 671 " --> pdb=" O MET D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 679 No H-bonds generated for 'chain 'D' and resid 677 through 679' Processing helix chain 'D' and resid 693 through 711 removed outlier: 5.009A pdb=" N ASP D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN D 699 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU D 703 " --> pdb=" O GLN D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 754 through 757 No H-bonds generated for 'chain 'D' and resid 754 through 757' Processing helix chain 'D' and resid 782 through 792 Processing helix chain 'D' and resid 814 through 827 removed outlier: 3.702A pdb=" N VAL D 818 " --> pdb=" O ILE D 814 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 819 " --> pdb=" O GLU D 815 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 820 " --> pdb=" O ALA D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 844 removed outlier: 3.925A pdb=" N ASN D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 857 Processing helix chain 'D' and resid 877 through 881 Processing helix chain 'D' and resid 884 through 888 removed outlier: 4.400A pdb=" N ASP D 887 " --> pdb=" O ILE D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 916 Processing helix chain 'D' and resid 1324 through 1337 Processing helix chain 'D' and resid 1343 through 1359 Processing helix chain 'D' and resid 1368 through 1376 Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 431 through 434 No H-bonds generated for 'chain 'E' and resid 431 through 434' Processing helix chain 'E' and resid 460 through 469 Processing helix chain 'E' and resid 496 through 506 Processing helix chain 'E' and resid 520 through 523 No H-bonds generated for 'chain 'E' and resid 520 through 523' Processing helix chain 'E' and resid 540 through 546 Processing helix chain 'E' and resid 569 through 571 No H-bonds generated for 'chain 'E' and resid 569 through 571' Processing helix chain 'E' and resid 590 through 597 Processing helix chain 'E' and resid 608 through 615 Processing helix chain 'E' and resid 624 through 641 Processing helix chain 'E' and resid 663 through 670 Processing helix chain 'E' and resid 693 through 696 No H-bonds generated for 'chain 'E' and resid 693 through 696' Processing helix chain 'E' and resid 701 through 711 Processing helix chain 'E' and resid 724 through 727 No H-bonds generated for 'chain 'E' and resid 724 through 727' Processing helix chain 'E' and resid 759 through 766 removed outlier: 4.250A pdb=" N GLN E 766 " --> pdb=" O MET E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 782 through 792 removed outlier: 3.744A pdb=" N ALA E 787 " --> pdb=" O GLN E 783 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 827 Processing helix chain 'E' and resid 838 through 841 No H-bonds generated for 'chain 'E' and resid 838 through 841' Processing helix chain 'E' and resid 847 through 858 Processing helix chain 'E' and resid 877 through 881 removed outlier: 3.645A pdb=" N LYS E 881 " --> pdb=" O SER E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 888 No H-bonds generated for 'chain 'E' and resid 886 through 888' Processing helix chain 'E' and resid 902 through 916 removed outlier: 4.352A pdb=" N ASN E 911 " --> pdb=" O ARG E 907 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU E 912 " --> pdb=" O TYR E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 1324 through 1337 Processing helix chain 'E' and resid 1343 through 1359 Processing helix chain 'E' and resid 1367 through 1376 removed outlier: 3.966A pdb=" N ASP E1371 " --> pdb=" O THR E1367 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 419 through 426 removed outlier: 3.928A pdb=" N LYS F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 434 Processing helix chain 'F' and resid 461 through 468 Processing helix chain 'F' and resid 493 through 509 removed outlier: 4.111A pdb=" N GLU F 497 " --> pdb=" O VAL F 493 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG F 498 " --> pdb=" O GLY F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 523 No H-bonds generated for 'chain 'F' and resid 520 through 523' Processing helix chain 'F' and resid 540 through 546 Processing helix chain 'F' and resid 564 through 566 No H-bonds generated for 'chain 'F' and resid 564 through 566' Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.673A pdb=" N THR F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 613 Processing helix chain 'F' and resid 625 through 641 Processing helix chain 'F' and resid 644 through 647 No H-bonds generated for 'chain 'F' and resid 644 through 647' Processing helix chain 'F' and resid 663 through 667 Processing helix chain 'F' and resid 692 through 710 removed outlier: 4.947A pdb=" N ALA F 697 " --> pdb=" O PRO F 694 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP F 698 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 700 " --> pdb=" O ALA F 697 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN F 702 " --> pdb=" O GLN F 699 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET F 710 " --> pdb=" O LEU F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 730 Processing helix chain 'F' and resid 754 through 766 removed outlier: 3.616A pdb=" N SER F 761 " --> pdb=" O GLU F 757 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN F 766 " --> pdb=" O MET F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 792 removed outlier: 3.970A pdb=" N ALA F 787 " --> pdb=" O GLN F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 803 through 806 No H-bonds generated for 'chain 'F' and resid 803 through 806' Processing helix chain 'F' and resid 814 through 827 Processing helix chain 'F' and resid 838 through 844 removed outlier: 4.090A pdb=" N ASN F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 847 through 858 Processing helix chain 'F' and resid 877 through 881 removed outlier: 4.442A pdb=" N LYS F 881 " --> pdb=" O SER F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 886 through 888 No H-bonds generated for 'chain 'F' and resid 886 through 888' Processing helix chain 'F' and resid 902 through 916 removed outlier: 3.756A pdb=" N TYR F 908 " --> pdb=" O ASN F 904 " (cutoff:3.500A) Processing helix chain 'F' and resid 1324 through 1337 Processing helix chain 'F' and resid 1343 through 1359 Processing helix chain 'F' and resid 1367 through 1376 Processing helix chain 'G' and resid 956 through 993 removed outlier: 4.123A pdb=" N GLY G 985 " --> pdb=" O ILE G 981 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU G 989 " --> pdb=" O GLY G 985 " (cutoff:3.500A) Processing helix chain 'G' and resid 1004 through 1008 Processing helix chain 'G' and resid 1050 through 1055 removed outlier: 3.700A pdb=" N ASN G1055 " --> pdb=" O GLU G1051 " (cutoff:3.500A) Processing helix chain 'G' and resid 1061 through 1077 Processing helix chain 'G' and resid 1081 through 1101 removed outlier: 3.803A pdb=" N GLU G1100 " --> pdb=" O MET G1096 " (cutoff:3.500A) Processing helix chain 'G' and resid 1104 through 1130 Processing sheet with id= A, first strand: chain 'A' and resid 580 through 584 removed outlier: 6.683A pdb=" N THR A 480 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE A 517 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE A 482 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP A 519 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG A 484 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 772 through 777 removed outlier: 8.009A pdb=" N LEU A 773 " --> pdb=" O ILE A 867 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 869 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE A 775 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS A 871 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLY A 777 " --> pdb=" O CYS A 871 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 873 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER A 832 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 870 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 834 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU A 872 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 836 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N GLU A 874 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN A 798 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE A 835 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN A 800 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 579 through 583 removed outlier: 3.564A pdb=" N GLY B 454 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER B 513 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE B 558 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 515 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA B 560 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 517 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR B 479 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE B 516 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE B 481 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP B 518 " --> pdb=" O PHE B 481 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 483 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 894 through 897 removed outlier: 7.847A pdb=" N PHE B 895 " --> pdb=" O ARG B 771 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU B 773 " --> pdb=" O PHE B 895 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B 897 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN B 775 " --> pdb=" O LEU B 897 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU B 772 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 868 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE B 774 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS B 870 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLY B 776 " --> pdb=" O CYS B 870 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 872 " --> pdb=" O GLY B 776 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER B 831 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 869 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 833 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU B 871 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 835 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLU B 873 " --> pdb=" O ILE B 835 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN B 797 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE B 834 " --> pdb=" O ASN B 797 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN B 799 " --> pdb=" O PHE B 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 579 through 583 removed outlier: 6.170A pdb=" N VAL C 557 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE C 452 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY C 559 " --> pdb=" O PHE C 452 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLY C 454 " --> pdb=" O GLY C 559 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 561 " --> pdb=" O GLY C 454 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 556 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR C 479 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE C 516 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE C 481 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP C 518 " --> pdb=" O PHE C 481 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG C 483 " --> pdb=" O ASP C 518 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 894 through 897 removed outlier: 7.545A pdb=" N PHE C 895 " --> pdb=" O ARG C 771 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU C 773 " --> pdb=" O PHE C 895 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU C 897 " --> pdb=" O LEU C 773 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN C 775 " --> pdb=" O LEU C 897 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU C 772 " --> pdb=" O ILE C 866 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 868 " --> pdb=" O LEU C 772 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE C 774 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS C 870 " --> pdb=" O ILE C 774 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY C 776 " --> pdb=" O CYS C 870 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 872 " --> pdb=" O GLY C 776 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER C 831 " --> pdb=" O LEU C 867 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 869 " --> pdb=" O SER C 831 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 833 " --> pdb=" O LEU C 869 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU C 871 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 835 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLU C 873 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN C 797 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE C 834 " --> pdb=" O ASN C 797 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN C 799 " --> pdb=" O PHE C 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 579 through 583 removed outlier: 3.947A pdb=" N GLY D 454 " --> pdb=" O THR D 561 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER D 513 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE D 558 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 515 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA D 560 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE D 517 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 894 through 897 removed outlier: 7.710A pdb=" N PHE D 895 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU D 773 " --> pdb=" O PHE D 895 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 897 " --> pdb=" O LEU D 773 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN D 775 " --> pdb=" O LEU D 897 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU D 772 " --> pdb=" O ILE D 866 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU D 868 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE D 774 " --> pdb=" O LEU D 868 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS D 870 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY D 776 " --> pdb=" O CYS D 870 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA D 872 " --> pdb=" O GLY D 776 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER D 831 " --> pdb=" O LEU D 867 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU D 869 " --> pdb=" O SER D 831 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL D 833 " --> pdb=" O LEU D 869 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU D 871 " --> pdb=" O VAL D 833 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE D 835 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N GLU D 873 " --> pdb=" O ILE D 835 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN D 797 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE D 834 " --> pdb=" O ASN D 797 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLN D 799 " --> pdb=" O PHE D 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 579 through 583 removed outlier: 6.397A pdb=" N VAL E 557 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE E 452 " --> pdb=" O VAL E 557 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY E 559 " --> pdb=" O PHE E 452 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY E 454 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE E 515 " --> pdb=" O ILE E 558 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ALA E 560 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE E 517 " --> pdb=" O ALA E 560 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 894 through 897 removed outlier: 7.671A pdb=" N PHE E 895 " --> pdb=" O ARG E 771 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU E 773 " --> pdb=" O PHE E 895 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU E 897 " --> pdb=" O LEU E 773 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN E 775 " --> pdb=" O LEU E 897 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU E 772 " --> pdb=" O ILE E 866 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU E 868 " --> pdb=" O LEU E 772 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE E 774 " --> pdb=" O LEU E 868 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS E 870 " --> pdb=" O ILE E 774 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLY E 776 " --> pdb=" O CYS E 870 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA E 872 " --> pdb=" O GLY E 776 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER E 831 " --> pdb=" O LEU E 867 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU E 869 " --> pdb=" O SER E 831 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL E 833 " --> pdb=" O LEU E 869 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU E 871 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE E 835 " --> pdb=" O LEU E 871 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLU E 873 " --> pdb=" O ILE E 835 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN E 797 " --> pdb=" O VAL E 832 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE E 834 " --> pdb=" O ASN E 797 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN E 799 " --> pdb=" O PHE E 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 579 through 583 removed outlier: 6.777A pdb=" N SER F 513 " --> pdb=" O ILE F 556 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE F 558 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE F 515 " --> pdb=" O ILE F 558 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA F 560 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE F 517 " --> pdb=" O ALA F 560 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR F 479 " --> pdb=" O ILE F 514 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE F 516 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE F 481 " --> pdb=" O PHE F 516 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 894 through 897 removed outlier: 7.628A pdb=" N PHE F 895 " --> pdb=" O ARG F 771 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU F 773 " --> pdb=" O PHE F 895 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU F 897 " --> pdb=" O LEU F 773 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN F 775 " --> pdb=" O LEU F 897 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU F 772 " --> pdb=" O ILE F 866 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU F 868 " --> pdb=" O LEU F 772 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE F 774 " --> pdb=" O LEU F 868 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS F 870 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLY F 776 " --> pdb=" O CYS F 870 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA F 872 " --> pdb=" O GLY F 776 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER F 831 " --> pdb=" O LEU F 867 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU F 869 " --> pdb=" O SER F 831 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL F 833 " --> pdb=" O LEU F 869 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU F 871 " --> pdb=" O VAL F 833 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE F 835 " --> pdb=" O LEU F 871 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU F 873 " --> pdb=" O ILE F 835 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN F 797 " --> pdb=" O VAL F 832 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE F 834 " --> pdb=" O ASN F 797 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN F 799 " --> pdb=" O PHE F 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'G' and resid 1025 through 1027 944 hydrogen bonds defined for protein. 2670 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: 9.26 Time building geometry restraints manager: 11.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4850 1.31 - 1.43: 7285 1.43 - 1.56: 17375 1.56 - 1.69: 19 1.69 - 1.82: 179 Bond restraints: 29708 Sorted by residual: bond pdb=" CA PHE F 577 " pdb=" C PHE F 577 " ideal model delta sigma weight residual 1.532 1.457 0.075 9.60e-03 1.09e+04 6.09e+01 bond pdb=" C VAL B 410 " pdb=" O VAL B 410 " ideal model delta sigma weight residual 1.236 1.178 0.059 1.04e-02 9.25e+03 3.17e+01 bond pdb=" N ASN B 409 " pdb=" CA ASN B 409 " ideal model delta sigma weight residual 1.463 1.396 0.067 1.30e-02 5.92e+03 2.63e+01 bond pdb=" C MET B 408 " pdb=" O MET B 408 " ideal model delta sigma weight residual 1.234 1.181 0.053 1.07e-02 8.73e+03 2.45e+01 bond pdb=" CA MET B 408 " pdb=" C MET B 408 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.34e-02 5.57e+03 2.06e+01 ... (remaining 29703 not shown) Histogram of bond angle deviations from ideal: 97.46 - 105.13: 676 105.13 - 112.80: 15466 112.80 - 120.47: 13144 120.47 - 128.14: 10690 128.14 - 135.81: 164 Bond angle restraints: 40140 Sorted by residual: angle pdb=" N PHE F 577 " pdb=" CA PHE F 577 " pdb=" C PHE F 577 " ideal model delta sigma weight residual 110.91 100.67 10.24 1.17e+00 7.31e-01 7.65e+01 angle pdb=" N LEU G1118 " pdb=" CA LEU G1118 " pdb=" C LEU G1118 " ideal model delta sigma weight residual 111.14 103.34 7.80 1.08e+00 8.57e-01 5.21e+01 angle pdb=" N MET B 408 " pdb=" CA MET B 408 " pdb=" C MET B 408 " ideal model delta sigma weight residual 109.79 119.76 -9.97 1.56e+00 4.11e-01 4.08e+01 angle pdb=" N ASP F 550 " pdb=" CA ASP F 550 " pdb=" CB ASP F 550 " ideal model delta sigma weight residual 114.17 107.62 6.55 1.14e+00 7.69e-01 3.30e+01 angle pdb=" CB MET B 408 " pdb=" CG MET B 408 " pdb=" SD MET B 408 " ideal model delta sigma weight residual 112.70 97.46 15.24 3.00e+00 1.11e-01 2.58e+01 ... (remaining 40135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 17828 34.80 - 69.60: 469 69.60 - 104.39: 47 104.39 - 139.19: 3 139.19 - 173.99: 1 Dihedral angle restraints: 18348 sinusoidal: 7704 harmonic: 10644 Sorted by residual: dihedral pdb=" CA LYS D 491 " pdb=" C LYS D 491 " pdb=" N TRP D 492 " pdb=" CA TRP D 492 " ideal model delta harmonic sigma weight residual -180.00 -138.07 -41.93 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA LYS B 927 " pdb=" C LYS B 927 " pdb=" N ARG B 928 " pdb=" CA ARG B 928 " ideal model delta harmonic sigma weight residual 180.00 144.21 35.79 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA GLN C 511 " pdb=" C GLN C 511 " pdb=" N PRO C 512 " pdb=" CA PRO C 512 " ideal model delta harmonic sigma weight residual 180.00 144.67 35.33 0 5.00e+00 4.00e-02 4.99e+01 ... (remaining 18345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4167 0.092 - 0.184: 364 0.184 - 0.276: 14 0.276 - 0.368: 2 0.368 - 0.461: 2 Chirality restraints: 4549 Sorted by residual: chirality pdb=" CA ASP B 407 " pdb=" N ASP B 407 " pdb=" C ASP B 407 " pdb=" CB ASP B 407 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA MET B 408 " pdb=" N MET B 408 " pdb=" C MET B 408 " pdb=" CB MET B 408 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB VAL E 930 " pdb=" CA VAL E 930 " pdb=" CG1 VAL E 930 " pdb=" CG2 VAL E 930 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 4546 not shown) Planarity restraints: 5129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 511 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO C 512 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 512 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 512 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 693 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO B 694 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 407 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ASP B 407 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP B 407 " -0.020 2.00e-02 2.50e+03 pdb=" N MET B 408 " -0.017 2.00e-02 2.50e+03 ... (remaining 5126 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6999 2.79 - 3.32: 26609 3.32 - 3.84: 48301 3.84 - 4.37: 56700 4.37 - 4.90: 94681 Nonbonded interactions: 233290 Sorted by model distance: nonbonded pdb=" O PRO B 455 " pdb=" OG1 THR B 458 " model vdw 2.262 2.440 nonbonded pdb=" OD2 ASP B 407 " pdb=" CD2 PHE B 480 " model vdw 2.292 3.340 nonbonded pdb=" OG SER C 528 " pdb=" O LYS C 530 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR A 717 " pdb=" O GLN A 720 " model vdw 2.294 2.440 nonbonded pdb=" O LYS G1040 " pdb=" OG1 THR G1077 " model vdw 2.300 2.440 ... (remaining 233285 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 410 through 487 or resid 496 through 526 or resid 539 thro \ ugh 733 or resid 752 through 1379)) selection = (chain 'B' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) selection = (chain 'C' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) selection = (chain 'D' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 1378)) selection = (chain 'E' and (resid 409 through 732 or resid 751 through 1378)) selection = (chain 'F' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 108 5.16 5 C 18652 2.51 5 N 4953 2.21 5 O 5419 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.760 Check model and map are aligned: 0.420 Process input model: 69.840 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.270 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 0.075 29708 Z= 0.351 Angle : 0.940 15.240 40140 Z= 0.506 Chirality : 0.054 0.461 4549 Planarity : 0.008 0.107 5129 Dihedral : 16.270 173.988 11394 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.11), residues: 3583 helix: -2.97 (0.08), residues: 1747 sheet: -2.05 (0.24), residues: 381 loop : -2.74 (0.14), residues: 1455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 640 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 650 average time/residue: 0.4920 time to fit residues: 474.9985 Evaluate side-chains 346 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 343 time to evaluate : 3.481 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2465 time to fit residues: 6.4177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 183 optimal weight: 0.0870 chunk 144 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 208 optimal weight: 0.1980 chunk 325 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 687 GLN A 703 ASN A 713 ASN A 727 GLN A 781 ASN A 800 GLN A 849 ASN A1346 GLN A1351 HIS B 420 ASN B 533 GLN B 639 GLN B 702 ASN B 820 GLN C 424 GLN C 443 ASN C 510 HIS ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN C 562 ASN C 712 ASN C 727 ASN C 799 GLN C 820 GLN C1345 GLN C1350 HIS D 780 ASN D 799 GLN D 904 ASN E 443 ASN E 551 ASN E 727 ASN E 775 ASN E 896 GLN E1340 ASN E1345 GLN F 440 GLN F 443 ASN F 686 GLN F 719 GLN F 727 ASN F 829 GLN F 848 ASN F 904 ASN F1345 GLN F1350 HIS G 977 ASN G1055 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29708 Z= 0.175 Angle : 0.602 9.048 40140 Z= 0.296 Chirality : 0.042 0.211 4549 Planarity : 0.005 0.087 5129 Dihedral : 7.488 167.571 3928 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.13), residues: 3583 helix: -1.46 (0.11), residues: 1736 sheet: -1.74 (0.25), residues: 381 loop : -2.13 (0.16), residues: 1466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 366 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 393 average time/residue: 0.4561 time to fit residues: 278.1070 Evaluate side-chains 323 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 303 time to evaluate : 3.609 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2724 time to fit residues: 15.5984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 chunk 351 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 322 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN B1350 HIS C 510 HIS C 531 GLN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 GLN D1350 HIS E1340 ASN E1350 HIS F 562 ASN F 904 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 29708 Z= 0.193 Angle : 0.584 8.356 40140 Z= 0.283 Chirality : 0.042 0.184 4549 Planarity : 0.005 0.086 5129 Dihedral : 6.927 154.154 3928 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3583 helix: -0.58 (0.12), residues: 1749 sheet: -1.44 (0.26), residues: 365 loop : -1.72 (0.16), residues: 1469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 323 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 23 residues processed: 370 average time/residue: 0.4656 time to fit residues: 273.7111 Evaluate side-chains 308 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 285 time to evaluate : 3.538 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3002 time to fit residues: 17.9660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 0.8980 chunk 244 optimal weight: 0.0670 chunk 169 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 218 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 170 optimal weight: 0.0770 chunk 309 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS A 800 GLN B 829 GLN C 510 HIS C 531 GLN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 791 ASN E1340 ASN F 440 GLN F 443 ASN ** F1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 29708 Z= 0.154 Angle : 0.554 10.866 40140 Z= 0.266 Chirality : 0.041 0.163 4549 Planarity : 0.004 0.080 5129 Dihedral : 6.542 146.349 3928 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3583 helix: -0.11 (0.13), residues: 1737 sheet: -1.14 (0.27), residues: 354 loop : -1.48 (0.17), residues: 1492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 303 time to evaluate : 3.241 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 327 average time/residue: 0.4551 time to fit residues: 236.3904 Evaluate side-chains 294 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 278 time to evaluate : 3.598 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2755 time to fit residues: 13.1389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN B 896 GLN C 510 HIS ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN E1340 ASN ** F1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 29708 Z= 0.220 Angle : 0.582 9.260 40140 Z= 0.279 Chirality : 0.042 0.155 4549 Planarity : 0.004 0.078 5129 Dihedral : 6.532 147.342 3928 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3583 helix: 0.01 (0.13), residues: 1744 sheet: -1.11 (0.27), residues: 355 loop : -1.37 (0.17), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 296 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 320 average time/residue: 0.4462 time to fit residues: 226.2556 Evaluate side-chains 291 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 277 time to evaluate : 3.563 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3247 time to fit residues: 13.0455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 9.9990 chunk 311 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 346 optimal weight: 0.0980 chunk 287 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 HIS D 510 HIS D 535 HIS E 510 HIS E1340 ASN F 443 ASN F1326 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 29708 Z= 0.173 Angle : 0.558 9.435 40140 Z= 0.268 Chirality : 0.041 0.144 4549 Planarity : 0.004 0.083 5129 Dihedral : 6.358 147.176 3928 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.83 (0.14), residues: 3583 helix: 0.20 (0.13), residues: 1751 sheet: -0.99 (0.27), residues: 353 loop : -1.26 (0.17), residues: 1479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 290 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 309 average time/residue: 0.4581 time to fit residues: 226.3714 Evaluate side-chains 282 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 273 time to evaluate : 4.319 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3007 time to fit residues: 9.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 252 optimal weight: 0.4980 chunk 195 optimal weight: 4.9990 chunk 291 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 210 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN C 510 HIS E 510 HIS E1337 HIS E1340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 29708 Z= 0.158 Angle : 0.545 8.872 40140 Z= 0.261 Chirality : 0.041 0.184 4549 Planarity : 0.004 0.079 5129 Dihedral : 6.219 147.266 3928 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3583 helix: 0.34 (0.13), residues: 1754 sheet: -0.83 (0.27), residues: 350 loop : -1.17 (0.17), residues: 1479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 292 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 311 average time/residue: 0.4432 time to fit residues: 221.4627 Evaluate side-chains 289 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 3.757 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3080 time to fit residues: 15.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 235 optimal weight: 0.0970 chunk 170 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN A 838 ASN B1326 GLN C 510 HIS D1326 GLN E 510 HIS E1340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 29708 Z= 0.209 Angle : 0.573 9.564 40140 Z= 0.275 Chirality : 0.041 0.150 4549 Planarity : 0.004 0.077 5129 Dihedral : 6.284 147.548 3928 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3583 helix: 0.30 (0.13), residues: 1762 sheet: -0.80 (0.27), residues: 353 loop : -1.10 (0.17), residues: 1468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 282 time to evaluate : 3.824 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 291 average time/residue: 0.4649 time to fit residues: 216.2123 Evaluate side-chains 271 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 266 time to evaluate : 3.398 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3101 time to fit residues: 7.5321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 301 optimal weight: 6.9990 chunk 321 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 290 optimal weight: 0.2980 chunk 304 optimal weight: 2.9990 chunk 320 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN B1326 GLN C 510 HIS E 510 HIS E 511 GLN E 829 GLN E1340 ASN ** F 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 29708 Z= 0.157 Angle : 0.552 10.103 40140 Z= 0.264 Chirality : 0.040 0.143 4549 Planarity : 0.004 0.078 5129 Dihedral : 6.119 144.699 3928 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3583 helix: 0.49 (0.13), residues: 1749 sheet: -0.70 (0.27), residues: 368 loop : -0.99 (0.17), residues: 1466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 284 time to evaluate : 3.457 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 289 average time/residue: 0.4717 time to fit residues: 218.2090 Evaluate side-chains 273 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 265 time to evaluate : 3.517 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3588 time to fit residues: 9.6122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 0.9980 chunk 340 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 236 optimal weight: 0.0000 chunk 356 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN B1326 GLN C 510 HIS ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1340 ASN ** F 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 29708 Z= 0.176 Angle : 0.559 8.725 40140 Z= 0.267 Chirality : 0.041 0.153 4549 Planarity : 0.004 0.075 5129 Dihedral : 6.091 142.260 3928 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3583 helix: 0.49 (0.13), residues: 1763 sheet: -0.69 (0.27), residues: 368 loop : -0.91 (0.18), residues: 1452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 274 time to evaluate : 3.350 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 278 average time/residue: 0.4653 time to fit residues: 205.3951 Evaluate side-chains 270 residues out of total 3268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 268 time to evaluate : 3.650 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3069 time to fit residues: 6.1472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 3.9990 chunk 302 optimal weight: 0.0020 chunk 87 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 78 optimal weight: 0.0980 chunk 284 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.0270 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN A 883 ASN B1326 GLN C 510 HIS ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1340 ASN F 598 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.195896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139310 restraints weight = 35415.948| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.18 r_work: 0.3432 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 29708 Z= 0.136 Angle : 0.541 11.443 40140 Z= 0.258 Chirality : 0.040 0.144 4549 Planarity : 0.004 0.078 5129 Dihedral : 5.889 137.826 3928 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3583 helix: 0.65 (0.13), residues: 1759 sheet: -0.56 (0.28), residues: 338 loop : -0.88 (0.18), residues: 1486 =============================================================================== Job complete usr+sys time: 6705.22 seconds wall clock time: 123 minutes 7.27 seconds (7387.27 seconds total)