Starting phenix.real_space_refine on Wed Jul 24 09:01:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/07_2024/8juw_36665_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/07_2024/8juw_36665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/07_2024/8juw_36665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/07_2024/8juw_36665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/07_2024/8juw_36665_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/07_2024/8juw_36665_neut.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 110 5.16 5 C 16134 2.51 5 N 4362 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 867": "OE1" <-> "OE2" Residue "A GLU 906": "OE1" <-> "OE2" Residue "A TYR 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1380": "OE1" <-> "OE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 563": "OD1" <-> "OD2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 826": "OD1" <-> "OD2" Residue "B GLU 840": "OE1" <-> "OE2" Residue "B GLU 905": "OE1" <-> "OE2" Residue "B ASP 935": "OD1" <-> "OD2" Residue "B GLU 1331": "OE1" <-> "OE2" Residue "B GLU 1382": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C ASP 534": "OD1" <-> "OD2" Residue "C PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 840": "OE1" <-> "OE2" Residue "C PHE 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1353": "OE1" <-> "OE2" Residue "C TYR 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D ASP 531": "OD1" <-> "OD2" Residue "D ASP 534": "OD1" <-> "OD2" Residue "D TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 839": "OE1" <-> "OE2" Residue "D GLU 867": "OE1" <-> "OE2" Residue "D GLU 1353": "OE1" <-> "OE2" Residue "E ASP 500": "OD1" <-> "OD2" Residue "E ASP 531": "OD1" <-> "OD2" Residue "E ASP 545": "OD1" <-> "OD2" Residue "E GLU 567": "OE1" <-> "OE2" Residue "E PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 645": "OE1" <-> "OE2" Residue "E GLU 800": "OE1" <-> "OE2" Residue "E GLU 840": "OE1" <-> "OE2" Residue "E GLU 905": "OE1" <-> "OE2" Residue "E PHE 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 935": "OD1" <-> "OD2" Residue "E TYR 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 453": "OE1" <-> "OE2" Residue "F ASP 678": "OD1" <-> "OD2" Residue "F TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 914": "OD1" <-> "OD2" Residue "F GLU 934": "OE1" <-> "OE2" Residue "F TYR 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25282 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4157 Classifications: {'peptide': 523} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 487} Chain breaks: 5 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4199 Classifications: {'peptide': 528} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 493} Chain breaks: 2 Chain: "D" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4213 Classifications: {'peptide': 530} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 495} Chain breaks: 2 Chain: "E" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4202 Classifications: {'peptide': 528} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "F" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 483} Chain breaks: 4 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.16, per 1000 atoms: 0.56 Number of scatterers: 25282 At special positions: 0 Unit cell: (125.4, 165, 149.6, 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 110 16.00 P 17 15.00 O 4659 8.00 N 4362 7.00 C 16134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.67 Conformation dependent library (CDL) restraints added in 4.6 seconds 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 12 sheets defined 52.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.789A pdb=" N GLU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 507 through 524 removed outlier: 4.146A pdb=" N ARG A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 536 Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 576 through 580 removed outlier: 4.046A pdb=" N SER A 579 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 580 " --> pdb=" O LEU A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 580' Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.860A pdb=" N ALA A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 685 removed outlier: 3.912A pdb=" N VAL A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 6.337A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 4.023A pdb=" N GLU A 728 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 729 " --> pdb=" O HIS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 837 through 852 removed outlier: 4.373A pdb=" N THR A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 870 through 881 Processing helix chain 'A' and resid 899 through 903 Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 910 through 911 No H-bonds generated for 'chain 'A' and resid 910 through 911' Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 926 through 938 removed outlier: 4.746A pdb=" N ASP A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU A 936 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 3.944A pdb=" N LYS A 943 " --> pdb=" O GLN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1344 removed outlier: 4.050A pdb=" N ASN A1335 " --> pdb=" O GLU A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1365 removed outlier: 3.904A pdb=" N TYR A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A1357 " --> pdb=" O GLU A1353 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A1361 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1386 removed outlier: 4.814A pdb=" N GLU A1384 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 removed outlier: 3.732A pdb=" N MET B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 447 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.511A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 removed outlier: 3.967A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 523 removed outlier: 4.296A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.571A pdb=" N GLY B 535 " --> pdb=" O GLN B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 560 removed outlier: 4.035A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 removed outlier: 3.664A pdb=" N SER B 579 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.677A pdb=" N ARG B 604 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 605 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 606 " --> pdb=" O GLU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.682A pdb=" N ASN B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.781A pdb=" N ALA B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 656 through 659 removed outlier: 4.601A pdb=" N TYR B 659 " --> pdb=" O PRO B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 659' Processing helix chain 'B' and resid 675 through 686 removed outlier: 3.851A pdb=" N PHE B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 724 removed outlier: 7.465A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N THR B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 728 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 837 through 852 Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 867 through 869 No H-bonds generated for 'chain 'B' and resid 867 through 869' Processing helix chain 'B' and resid 870 through 882 removed outlier: 3.504A pdb=" N GLN B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 903 removed outlier: 3.553A pdb=" N LEU B 903 " --> pdb=" O HIS B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 910 through 911 No H-bonds generated for 'chain 'B' and resid 910 through 911' Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 925 through 935 removed outlier: 4.467A pdb=" N ASP B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1344 removed outlier: 4.070A pdb=" N ASN B1335 " --> pdb=" O GLU B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1365 removed outlier: 3.754A pdb=" N ALA B1357 " --> pdb=" O GLU B1353 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B1362 " --> pdb=" O VAL B1358 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1386 removed outlier: 3.533A pdb=" N GLU B1384 " --> pdb=" O GLU B1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 443 removed outlier: 4.108A pdb=" N GLU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 448 Processing helix chain 'C' and resid 451 through 456 removed outlier: 4.190A pdb=" N PHE C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 486 removed outlier: 3.813A pdb=" N ALA C 477 " --> pdb=" O LYS C 473 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.809A pdb=" N ARG C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 536 Processing helix chain 'C' and resid 546 through 559 Processing helix chain 'C' and resid 576 through 580 removed outlier: 3.559A pdb=" N SER C 579 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 600 through 612 removed outlier: 3.800A pdb=" N LYS C 605 " --> pdb=" O LYS C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.840A pdb=" N GLU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.596A pdb=" N ALA C 644 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 647 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 685 removed outlier: 3.588A pdb=" N PHE C 679 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 724 removed outlier: 4.041A pdb=" N LEU C 709 " --> pdb=" O VAL C 705 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 710 " --> pdb=" O LYS C 706 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASN C 711 " --> pdb=" O PRO C 707 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR C 712 " --> pdb=" O LEU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 817 Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 837 through 852 removed outlier: 3.612A pdb=" N THR C 841 " --> pdb=" O SER C 837 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 846 " --> pdb=" O CYS C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 866 Processing helix chain 'C' and resid 870 through 881 removed outlier: 3.583A pdb=" N LEU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 903 Processing helix chain 'C' and resid 912 through 916 Processing helix chain 'C' and resid 925 through 939 removed outlier: 3.608A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 1331 through 1344 removed outlier: 3.955A pdb=" N ASN C1335 " --> pdb=" O GLU C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1366 removed outlier: 4.044A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1375 through 1385 Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.833A pdb=" N ALA D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 437 " --> pdb=" O ASN D 433 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 451 through 456 removed outlier: 4.386A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.781A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 523 removed outlier: 3.729A pdb=" N ARG D 511 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 521 " --> pdb=" O PHE D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 536 Processing helix chain 'D' and resid 546 through 560 removed outlier: 3.966A pdb=" N SER D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 558 " --> pdb=" O THR D 554 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP D 560 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 612 removed outlier: 5.504A pdb=" N LYS D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.871A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 655 removed outlier: 3.865A pdb=" N LYS D 640 " --> pdb=" O GLY D 636 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 659 removed outlier: 4.224A pdb=" N TYR D 659 " --> pdb=" O PRO D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 659' Processing helix chain 'D' and resid 677 through 685 removed outlier: 3.543A pdb=" N VAL D 681 " --> pdb=" O LYS D 677 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN D 684 " --> pdb=" O GLU D 680 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 removed outlier: 3.688A pdb=" N ARG D 692 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA D 693 " --> pdb=" O SER D 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 693' Processing helix chain 'D' and resid 705 through 724 removed outlier: 6.024A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N THR D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 817 Processing helix chain 'D' and resid 826 through 831 Processing helix chain 'D' and resid 837 through 852 removed outlier: 4.022A pdb=" N THR D 841 " --> pdb=" O SER D 837 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE D 846 " --> pdb=" O CYS D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 866 Processing helix chain 'D' and resid 870 through 881 removed outlier: 3.709A pdb=" N LEU D 881 " --> pdb=" O PHE D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 removed outlier: 3.972A pdb=" N LEU D 910 " --> pdb=" O GLU D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 916 Processing helix chain 'D' and resid 925 through 938 removed outlier: 3.650A pdb=" N ARG D 929 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1331 through 1344 removed outlier: 4.188A pdb=" N ASN D1335 " --> pdb=" O GLU D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1366 removed outlier: 3.530A pdb=" N CYS D1362 " --> pdb=" O VAL D1358 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS D1366 " --> pdb=" O CYS D1362 " (cutoff:3.500A) Processing helix chain 'D' and resid 1375 through 1386 Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.748A pdb=" N MET E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 450 through 455 removed outlier: 3.948A pdb=" N LYS E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE E 455 " --> pdb=" O VAL E 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 450 through 455' Processing helix chain 'E' and resid 474 through 486 Processing helix chain 'E' and resid 507 through 523 removed outlier: 4.744A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG E 514 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 536 Processing helix chain 'E' and resid 545 through 561 removed outlier: 3.892A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 612 Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.091A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 655 removed outlier: 3.861A pdb=" N CYS E 643 " --> pdb=" O ILE E 639 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA E 647 " --> pdb=" O CYS E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 686 removed outlier: 3.508A pdb=" N LYS E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 724 removed outlier: 6.940A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 817 Processing helix chain 'E' and resid 826 through 831 Processing helix chain 'E' and resid 837 through 852 removed outlier: 3.521A pdb=" N THR E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR E 852 " --> pdb=" O GLU E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 866 removed outlier: 3.548A pdb=" N TRP E 866 " --> pdb=" O ILE E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 870 through 881 removed outlier: 3.571A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 904 through 909 removed outlier: 3.782A pdb=" N GLU E 909 " --> pdb=" O GLU E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 911 No H-bonds generated for 'chain 'E' and resid 910 through 911' Processing helix chain 'E' and resid 912 through 916 Processing helix chain 'E' and resid 925 through 933 Processing helix chain 'E' and resid 1331 through 1344 Processing helix chain 'E' and resid 1348 through 1366 removed outlier: 3.641A pdb=" N HIS E1366 " --> pdb=" O CYS E1362 " (cutoff:3.500A) Processing helix chain 'E' and resid 1375 through 1386 Processing helix chain 'F' and resid 431 through 442 removed outlier: 3.643A pdb=" N ILE F 435 " --> pdb=" O LEU F 431 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 448 Processing helix chain 'F' and resid 472 through 486 removed outlier: 4.037A pdb=" N VAL F 476 " --> pdb=" O GLY F 472 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA F 477 " --> pdb=" O LYS F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 523 removed outlier: 4.022A pdb=" N ARG F 514 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR F 521 " --> pdb=" O PHE F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 537 removed outlier: 4.452A pdb=" N LEU F 536 " --> pdb=" O GLN F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 562 Processing helix chain 'F' and resid 602 through 612 removed outlier: 4.181A pdb=" N GLU F 606 " --> pdb=" O GLU F 602 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR F 612 " --> pdb=" O LEU F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 631 Processing helix chain 'F' and resid 636 through 654 removed outlier: 3.591A pdb=" N CYS F 643 " --> pdb=" O ILE F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.827A pdb=" N TYR F 659 " --> pdb=" O PRO F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 684 removed outlier: 4.250A pdb=" N PHE F 679 " --> pdb=" O SER F 675 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 724 removed outlier: 6.467A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 817 removed outlier: 3.670A pdb=" N ALA F 812 " --> pdb=" O HIS F 808 " (cutoff:3.500A) Processing helix chain 'F' and resid 826 through 831 Processing helix chain 'F' and resid 837 through 852 removed outlier: 3.540A pdb=" N THR F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 843 " --> pdb=" O GLU F 839 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN F 844 " --> pdb=" O GLU F 840 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE F 846 " --> pdb=" O CYS F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 866 Processing helix chain 'F' and resid 870 through 883 removed outlier: 3.618A pdb=" N LYS F 874 " --> pdb=" O GLY F 870 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 903 removed outlier: 3.602A pdb=" N LEU F 903 " --> pdb=" O HIS F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 904 through 909 Processing helix chain 'F' and resid 925 through 932 Processing helix chain 'F' and resid 1332 through 1344 Processing helix chain 'F' and resid 1345 through 1347 No H-bonds generated for 'chain 'F' and resid 1345 through 1347' Processing helix chain 'F' and resid 1348 through 1366 removed outlier: 3.792A pdb=" N CYS F1362 " --> pdb=" O VAL F1358 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE F1363 " --> pdb=" O ILE F1359 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F1364 " --> pdb=" O SER F1360 " (cutoff:3.500A) Processing helix chain 'F' and resid 1374 through 1386 removed outlier: 3.522A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.809A pdb=" N ALA A 492 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE A 529 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 494 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP A 531 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG A 496 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER A 526 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE A 571 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 528 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA A 573 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE A 530 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY A 462 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N PHE A 594 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 464 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 821 through 824 removed outlier: 6.561A pdb=" N THR A 821 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR A 858 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR A 823 " --> pdb=" O TYR A 858 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR A 895 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 795 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER A 896 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 797 " --> pdb=" O SER A 896 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 494 through 496 removed outlier: 6.761A pdb=" N PHE B 494 " --> pdb=" O PHE B 529 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 573 " --> pdb=" O PHE B 530 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824 removed outlier: 3.738A pdb=" N THR B 895 " --> pdb=" O VAL B 859 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 494 through 496 removed outlier: 3.699A pdb=" N VAL C 569 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 572 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 574 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY C 462 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N PHE C 594 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 464 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 821 through 824 removed outlier: 3.627A pdb=" N TYR C 858 " --> pdb=" O TYR C 823 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER C 855 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU C 893 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 857 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR C 895 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL C 859 " --> pdb=" O THR C 895 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 796 " --> pdb=" O PHE C 919 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.633A pdb=" N ALA D 492 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 529 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE D 494 " --> pdb=" O PHE D 529 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ASP D 531 " --> pdb=" O PHE D 494 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG D 496 " --> pdb=" O ASP D 531 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 572 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE D 594 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 821 through 824 removed outlier: 6.660A pdb=" N SER D 855 " --> pdb=" O LEU D 891 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU D 893 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL D 857 " --> pdb=" O LEU D 893 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR D 895 " --> pdb=" O VAL D 857 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE D 919 " --> pdb=" O ARG D 794 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU D 796 " --> pdb=" O PHE D 919 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 492 through 495 removed outlier: 6.514A pdb=" N ALA E 492 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE E 529 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE E 494 " --> pdb=" O PHE E 529 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP E 531 " --> pdb=" O PHE E 494 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL E 569 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS E 463 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 822 through 824 removed outlier: 3.686A pdb=" N THR E 895 " --> pdb=" O VAL E 859 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA E 894 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE E 919 " --> pdb=" O LEU E 796 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 492 through 497 removed outlier: 6.837A pdb=" N ALA F 492 " --> pdb=" O ILE F 527 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N PHE F 529 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE F 494 " --> pdb=" O PHE F 529 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP F 531 " --> pdb=" O PHE F 494 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG F 496 " --> pdb=" O ASP F 531 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER F 526 " --> pdb=" O VAL F 569 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE F 571 " --> pdb=" O SER F 526 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE F 528 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA F 573 " --> pdb=" O ILE F 528 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE F 530 " --> pdb=" O ALA F 573 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 821 through 824 removed outlier: 6.361A pdb=" N THR F 821 " --> pdb=" O ILE F 856 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR F 858 " --> pdb=" O THR F 821 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR F 823 " --> pdb=" O TYR F 858 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR F 895 " --> pdb=" O VAL F 859 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA F 894 " --> pdb=" O ILE F 795 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE F 919 " --> pdb=" O ARG F 794 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU F 796 " --> pdb=" O PHE F 919 " (cutoff:3.500A) 983 hydrogen bonds defined for protein. 2844 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: 8.66 Time building geometry restraints manager: 10.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8223 1.34 - 1.46: 4703 1.46 - 1.58: 12733 1.58 - 1.70: 19 1.70 - 1.82: 159 Bond restraints: 25837 Sorted by residual: bond pdb=" CG GLU A 934 " pdb=" CD GLU A 934 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.18e+00 bond pdb=" C LEU B 938 " pdb=" N LYS B 939 " ideal model delta sigma weight residual 1.332 1.305 0.027 1.40e-02 5.10e+03 3.74e+00 bond pdb=" CA THR D 574 " pdb=" CB THR D 574 " ideal model delta sigma weight residual 1.534 1.506 0.028 1.60e-02 3.91e+03 3.11e+00 bond pdb=" CG GLU E1382 " pdb=" CD GLU E1382 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.59e+00 bond pdb=" C LYS E 473 " pdb=" N THR E 474 " ideal model delta sigma weight residual 1.332 1.312 0.021 1.40e-02 5.10e+03 2.21e+00 ... (remaining 25832 not shown) Histogram of bond angle deviations from ideal: 98.11 - 106.46: 948 106.46 - 114.80: 15491 114.80 - 123.14: 17275 123.14 - 131.48: 1266 131.48 - 139.82: 45 Bond angle restraints: 35025 Sorted by residual: angle pdb=" N ILE F 672 " pdb=" CA ILE F 672 " pdb=" C ILE F 672 " ideal model delta sigma weight residual 111.91 105.77 6.14 8.90e-01 1.26e+00 4.76e+01 angle pdb=" N ILE B 868 " pdb=" CA ILE B 868 " pdb=" C ILE B 868 " ideal model delta sigma weight residual 113.71 108.22 5.49 9.50e-01 1.11e+00 3.33e+01 angle pdb=" C LEU E 624 " pdb=" N GLU E 625 " pdb=" CA GLU E 625 " ideal model delta sigma weight residual 121.14 112.56 8.58 1.75e+00 3.27e-01 2.40e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 113.10 108.99 4.11 9.70e-01 1.06e+00 1.79e+01 angle pdb=" C LYS C 473 " pdb=" N THR C 474 " pdb=" CA THR C 474 " ideal model delta sigma weight residual 121.14 115.03 6.11 1.75e+00 3.27e-01 1.22e+01 ... (remaining 35020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 15386 32.33 - 64.66: 467 64.66 - 96.99: 55 96.99 - 129.33: 0 129.33 - 161.66: 3 Dihedral angle restraints: 15911 sinusoidal: 6677 harmonic: 9234 Sorted by residual: dihedral pdb=" O2A ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PA ADP A1401 " pdb=" PB ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 101.66 -161.66 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 80.71 -140.71 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" O1B ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PB ADP A1401 " pdb=" PA ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 79.88 -139.89 1 2.00e+01 2.50e-03 4.24e+01 ... (remaining 15908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2808 0.048 - 0.097: 924 0.097 - 0.145: 201 0.145 - 0.193: 12 0.193 - 0.242: 4 Chirality restraints: 3949 Sorted by residual: chirality pdb=" CG LEU F 558 " pdb=" CB LEU F 558 " pdb=" CD1 LEU F 558 " pdb=" CD2 LEU F 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN A 616 " pdb=" N ASN A 616 " pdb=" C ASN A 616 " pdb=" CB ASN A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CG LEU E 938 " pdb=" CB LEU E 938 " pdb=" CD1 LEU E 938 " pdb=" CD2 LEU E 938 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3946 not shown) Planarity restraints: 4490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 787 " -0.062 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO E 788 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO E 788 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 788 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 468 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.28e+00 pdb=" N PRO D 469 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 944 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.94e+00 pdb=" N PRO C 945 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 945 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 945 " -0.046 5.00e-02 4.00e+02 ... (remaining 4487 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 392 2.66 - 3.22: 24341 3.22 - 3.78: 35578 3.78 - 4.34: 46804 4.34 - 4.90: 77539 Nonbonded interactions: 184654 Sorted by model distance: nonbonded pdb=" O GLN F 657 " pdb=" OG1 THR F 661 " model vdw 2.105 2.440 nonbonded pdb=" OH TYR D 655 " pdb=" OD1 ASP D 668 " model vdw 2.107 2.440 nonbonded pdb=" OH TYR F 655 " pdb=" O ASP F 668 " model vdw 2.124 2.440 nonbonded pdb=" NH1 ARG D 604 " pdb=" O CYS D 631 " model vdw 2.156 2.520 nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.174 2.440 ... (remaining 184649 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 422 through 598 or resid 601 through 688 or resid 696 thro \ ugh 727 or resid 787 through 943 or resid 1331 through 1388)) selection = (chain 'B' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'C' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'D' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'E' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923 or resid 925 through 943 or resid 1331 through \ 1388)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.940 Check model and map are aligned: 0.200 Set scattering table: 0.220 Process input model: 65.600 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.006 0.072 25837 Z= 0.406 Angle : 0.801 12.492 35025 Z= 0.422 Chirality : 0.048 0.242 3949 Planarity : 0.006 0.093 4490 Dihedral : 15.487 161.658 9887 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.46 % Favored : 91.38 % Rotamer: Outliers : 0.04 % Allowed : 0.61 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3110 helix: -0.12 (0.14), residues: 1399 sheet: 0.03 (0.28), residues: 375 loop : -1.65 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 505 HIS 0.008 0.001 HIS E 726 PHE 0.027 0.002 PHE B 831 TYR 0.019 0.002 TYR F 823 ARG 0.010 0.001 ARG B 794 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 409 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 MET cc_start: 0.7105 (tpt) cc_final: 0.6424 (tpp) REVERT: A 615 TRP cc_start: 0.4783 (m-10) cc_final: 0.4030 (m100) REVERT: A 686 MET cc_start: 0.2623 (pmm) cc_final: 0.2032 (pmm) REVERT: A 839 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6724 (tp30) REVERT: B 523 MET cc_start: 0.7638 (mpp) cc_final: 0.7099 (mtt) REVERT: F 441 MET cc_start: 0.5417 (ptm) cc_final: 0.4710 (ptt) REVERT: F 457 ILE cc_start: 0.7061 (mm) cc_final: 0.6822 (pt) REVERT: F 638 ASP cc_start: 0.4924 (p0) cc_final: 0.4399 (m-30) REVERT: F 686 MET cc_start: -0.0267 (pmm) cc_final: -0.1899 (ptm) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.4242 time to fit residues: 258.2531 Evaluate side-chains 186 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 9.9990 chunk 236 optimal weight: 0.2980 chunk 131 optimal weight: 0.0470 chunk 80 optimal weight: 0.0970 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1335 ASN A1354 ASN ** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 ASN B 434 HIS ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 HIS B 882 GLN B1330 HIS ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1366 HIS D 691 GLN D1330 HIS E 611 HIS ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 GLN ** F 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1377 GLN F1381 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25837 Z= 0.190 Angle : 0.663 11.748 35025 Z= 0.330 Chirality : 0.044 0.174 3949 Planarity : 0.005 0.056 4490 Dihedral : 9.517 174.796 3582 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.24 % Favored : 93.60 % Rotamer: Outliers : 1.26 % Allowed : 9.18 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.73 (0.15), residues: 3110 helix: 0.27 (0.14), residues: 1419 sheet: 0.24 (0.28), residues: 375 loop : -1.51 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 865 HIS 0.010 0.001 HIS B 611 PHE 0.019 0.001 PHE F 465 TYR 0.020 0.002 TYR A 448 ARG 0.012 0.001 ARG A1332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 232 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ARG cc_start: 0.6499 (ttp-110) cc_final: 0.6221 (mtm110) REVERT: A 615 TRP cc_start: 0.4407 (m-10) cc_final: 0.3958 (m100) REVERT: B 686 MET cc_start: 0.7645 (tmm) cc_final: 0.7435 (tmm) REVERT: E 546 GLN cc_start: 0.8317 (pp30) cc_final: 0.8070 (pt0) REVERT: F 441 MET cc_start: 0.4831 (ptm) cc_final: 0.4517 (ptt) REVERT: F 457 ILE cc_start: 0.7109 (mm) cc_final: 0.6742 (pt) REVERT: F 565 ARG cc_start: 0.2232 (pmt170) cc_final: 0.1682 (mpt180) REVERT: F 686 MET cc_start: -0.0175 (pmm) cc_final: -0.1569 (ptm) outliers start: 35 outliers final: 15 residues processed: 252 average time/residue: 0.3625 time to fit residues: 144.5993 Evaluate side-chains 201 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 631 CYS Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 862 ILE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain F residue 641 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 227 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A1354 ASN ** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN C1385 ASN ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1381 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25837 Z= 0.318 Angle : 0.676 10.574 35025 Z= 0.339 Chirality : 0.044 0.152 3949 Planarity : 0.005 0.054 4490 Dihedral : 9.222 177.781 3582 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 2.02 % Allowed : 11.77 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 3110 helix: 0.54 (0.14), residues: 1412 sheet: 0.11 (0.28), residues: 372 loop : -1.50 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 865 HIS 0.005 0.001 HIS D 434 PHE 0.028 0.002 PHE F 452 TYR 0.027 0.002 TYR F 448 ARG 0.005 0.001 ARG D 913 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 199 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 TRP cc_start: 0.5050 (m-10) cc_final: 0.4373 (m100) REVERT: A 1375 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6277 (pp) REVERT: B 651 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7829 (tp) REVERT: B 1379 MET cc_start: 0.6767 (mmt) cc_final: 0.6417 (mmt) REVERT: D 717 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8561 (mm) REVERT: E 543 ARG cc_start: 0.4627 (mmp-170) cc_final: 0.4182 (mmm160) REVERT: E 938 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5369 (pp) REVERT: F 441 MET cc_start: 0.4799 (ptm) cc_final: 0.4425 (ptt) REVERT: F 451 VAL cc_start: 0.6006 (t) cc_final: 0.5391 (t) REVERT: F 457 ILE cc_start: 0.7318 (mm) cc_final: 0.6926 (pt) REVERT: F 686 MET cc_start: -0.0154 (pmm) cc_final: -0.1602 (ptm) outliers start: 56 outliers final: 31 residues processed: 242 average time/residue: 0.3625 time to fit residues: 140.2674 Evaluate side-chains 208 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 1367 ARG Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 631 CYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 845 VAL Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 862 ILE Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 635 CYS Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 641 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 269 optimal weight: 30.0000 chunk 81 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** A1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1330 HIS E 546 GLN ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1381 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25837 Z= 0.213 Angle : 0.598 10.414 35025 Z= 0.295 Chirality : 0.042 0.163 3949 Planarity : 0.004 0.081 4490 Dihedral : 8.764 171.726 3582 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 2.34 % Allowed : 13.39 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.29 (0.16), residues: 3110 helix: 0.77 (0.15), residues: 1421 sheet: 0.26 (0.28), residues: 380 loop : -1.40 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 865 HIS 0.003 0.001 HIS A 815 PHE 0.021 0.001 PHE F 452 TYR 0.023 0.001 TYR A 858 ARG 0.007 0.000 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 187 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8462 (pp) REVERT: A 615 TRP cc_start: 0.5098 (m-10) cc_final: 0.4502 (m100) REVERT: A 1375 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.5515 (pp) REVERT: A 1379 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7468 (mtm) REVERT: B 651 LEU cc_start: 0.8065 (tt) cc_final: 0.7817 (tp) REVERT: B 1379 MET cc_start: 0.6770 (mmt) cc_final: 0.6304 (mmt) REVERT: C 455 PHE cc_start: 0.7263 (m-80) cc_final: 0.6744 (m-80) REVERT: D 717 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8474 (mm) REVERT: E 543 ARG cc_start: 0.4538 (mmp-170) cc_final: 0.4205 (mmm160) REVERT: E 546 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7341 (pp30) REVERT: E 819 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4952 (pttm) REVERT: E 938 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5495 (pp) REVERT: F 457 ILE cc_start: 0.7336 (mm) cc_final: 0.6970 (pt) REVERT: F 565 ARG cc_start: 0.2114 (pmt170) cc_final: 0.1311 (mtt180) REVERT: F 686 MET cc_start: -0.0078 (pmm) cc_final: -0.1372 (ptm) REVERT: F 823 TYR cc_start: 0.5817 (m-80) cc_final: 0.5582 (m-80) outliers start: 65 outliers final: 37 residues processed: 234 average time/residue: 0.3364 time to fit residues: 128.0849 Evaluate side-chains 210 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 1344 SER Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 546 GLN Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 641 SER Chi-restraints excluded: chain F residue 833 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.0670 chunk 171 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 224 optimal weight: 0.0040 chunk 124 optimal weight: 4.9990 chunk 257 optimal weight: 0.0970 chunk 208 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A1381 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1330 HIS ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1385 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25837 Z= 0.150 Angle : 0.566 10.104 35025 Z= 0.277 Chirality : 0.041 0.161 3949 Planarity : 0.004 0.069 4490 Dihedral : 8.317 167.861 3582 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.50 % Favored : 93.34 % Rotamer: Outliers : 1.91 % Allowed : 14.18 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.08 (0.16), residues: 3110 helix: 0.95 (0.15), residues: 1420 sheet: 0.48 (0.28), residues: 364 loop : -1.31 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 865 HIS 0.003 0.000 HIS A1330 PHE 0.020 0.001 PHE F 452 TYR 0.018 0.001 TYR A 448 ARG 0.010 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8341 (pp) REVERT: A 576 ARG cc_start: 0.6733 (ttp-110) cc_final: 0.6287 (mtm110) REVERT: A 615 TRP cc_start: 0.5220 (m-10) cc_final: 0.4638 (m100) REVERT: A 906 GLU cc_start: 0.6845 (tp30) cc_final: 0.5907 (tp30) REVERT: A 1375 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.5720 (pp) REVERT: A 1379 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7530 (mtm) REVERT: B 651 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7765 (tp) REVERT: C 455 PHE cc_start: 0.7115 (m-80) cc_final: 0.6715 (m-80) REVERT: D 717 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8574 (mm) REVERT: E 530 PHE cc_start: 0.5774 (m-80) cc_final: 0.5093 (m-10) REVERT: E 543 ARG cc_start: 0.4613 (mmp-170) cc_final: 0.4280 (mmm160) REVERT: E 819 LYS cc_start: 0.5211 (OUTLIER) cc_final: 0.4791 (pttm) REVERT: E 938 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5519 (pp) REVERT: F 457 ILE cc_start: 0.7203 (mm) cc_final: 0.6827 (pt) REVERT: F 495 MET cc_start: 0.2905 (ttt) cc_final: 0.2684 (mtp) REVERT: F 565 ARG cc_start: 0.2380 (pmt170) cc_final: 0.1732 (mpt180) REVERT: F 686 MET cc_start: -0.0289 (pmm) cc_final: -0.1527 (ptm) outliers start: 53 outliers final: 28 residues processed: 242 average time/residue: 0.3420 time to fit residues: 133.7376 Evaluate side-chains 215 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 1344 SER Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 833 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.7980 chunk 271 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 chunk 301 optimal weight: 0.5980 chunk 250 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25837 Z= 0.171 Angle : 0.578 12.467 35025 Z= 0.279 Chirality : 0.041 0.226 3949 Planarity : 0.004 0.065 4490 Dihedral : 8.069 162.370 3582 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.63 % Rotamer: Outliers : 2.02 % Allowed : 14.83 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.05 (0.16), residues: 3110 helix: 1.04 (0.15), residues: 1426 sheet: 0.56 (0.28), residues: 375 loop : -1.26 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 615 HIS 0.003 0.000 HIS A 815 PHE 0.017 0.001 PHE F 452 TYR 0.020 0.001 TYR F 823 ARG 0.006 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 184 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8373 (pp) REVERT: A 1375 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.5629 (pp) REVERT: A 1379 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7299 (mtm) REVERT: B 651 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7867 (tp) REVERT: B 1379 MET cc_start: 0.6790 (mmt) cc_final: 0.6331 (mmt) REVERT: C 455 PHE cc_start: 0.7127 (m-80) cc_final: 0.6612 (m-80) REVERT: D 717 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8550 (mm) REVERT: E 523 MET cc_start: 0.7677 (tpp) cc_final: 0.7342 (tpt) REVERT: E 543 ARG cc_start: 0.4509 (mmp-170) cc_final: 0.4169 (mmm160) REVERT: E 720 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6571 (pp) REVERT: E 819 LYS cc_start: 0.5364 (OUTLIER) cc_final: 0.4820 (pttm) REVERT: E 938 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5449 (pp) REVERT: F 457 ILE cc_start: 0.7304 (mm) cc_final: 0.6923 (pt) REVERT: F 565 ARG cc_start: 0.2178 (pmt170) cc_final: 0.1403 (mpt180) REVERT: F 659 TYR cc_start: 0.5368 (t80) cc_final: 0.5092 (m-80) REVERT: F 686 MET cc_start: -0.0135 (pmm) cc_final: -0.1509 (ptm) outliers start: 56 outliers final: 32 residues processed: 225 average time/residue: 0.3311 time to fit residues: 121.9249 Evaluate side-chains 209 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 641 SER Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 833 VAL Chi-restraints excluded: chain F residue 836 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 170 optimal weight: 0.4980 chunk 254 optimal weight: 0.0170 chunk 168 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 0.0970 chunk 183 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25837 Z= 0.151 Angle : 0.567 14.614 35025 Z= 0.272 Chirality : 0.040 0.201 3949 Planarity : 0.004 0.061 4490 Dihedral : 7.776 150.797 3582 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.57 % Rotamer: Outliers : 1.66 % Allowed : 15.65 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.14 (0.16), residues: 3110 helix: 1.10 (0.15), residues: 1427 sheet: 0.57 (0.28), residues: 369 loop : -1.18 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 615 HIS 0.002 0.000 HIS A 815 PHE 0.015 0.001 PHE F 452 TYR 0.016 0.001 TYR A 448 ARG 0.007 0.000 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8267 (pp) REVERT: A 576 ARG cc_start: 0.6741 (ttp-110) cc_final: 0.6266 (mtm110) REVERT: A 1375 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.5624 (pp) REVERT: A 1379 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7271 (mtm) REVERT: B 651 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7786 (tp) REVERT: B 1379 MET cc_start: 0.6782 (mmt) cc_final: 0.6324 (mmt) REVERT: C 455 PHE cc_start: 0.7135 (m-80) cc_final: 0.6658 (m-80) REVERT: E 543 ARG cc_start: 0.4524 (mmp-170) cc_final: 0.4211 (mmm160) REVERT: E 720 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6530 (pp) REVERT: E 819 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4828 (pttm) REVERT: E 938 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5522 (pp) REVERT: F 457 ILE cc_start: 0.7245 (mm) cc_final: 0.6856 (pt) REVERT: F 565 ARG cc_start: 0.2102 (pmt170) cc_final: 0.1372 (mpt180) REVERT: F 659 TYR cc_start: 0.5548 (t80) cc_final: 0.5091 (m-80) REVERT: F 683 MET cc_start: 0.3481 (mmt) cc_final: 0.3253 (mtt) REVERT: F 686 MET cc_start: -0.0180 (pmm) cc_final: -0.1477 (ptm) outliers start: 46 outliers final: 29 residues processed: 219 average time/residue: 0.3467 time to fit residues: 123.5757 Evaluate side-chains 209 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 833 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.0470 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 236 optimal weight: 9.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25837 Z= 0.155 Angle : 0.575 14.829 35025 Z= 0.277 Chirality : 0.040 0.183 3949 Planarity : 0.004 0.060 4490 Dihedral : 7.568 137.842 3582 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.63 % Rotamer: Outliers : 1.69 % Allowed : 15.98 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.20 (0.16), residues: 3110 helix: 1.15 (0.15), residues: 1430 sheet: 0.60 (0.28), residues: 374 loop : -1.17 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 615 HIS 0.003 0.000 HIS F 863 PHE 0.014 0.001 PHE F 452 TYR 0.017 0.001 TYR F 823 ARG 0.007 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 180 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8315 (pp) REVERT: A 576 ARG cc_start: 0.6712 (ttp-110) cc_final: 0.6270 (mtm110) REVERT: A 1375 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.5575 (pp) REVERT: A 1379 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7351 (mtm) REVERT: B 651 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7767 (tp) REVERT: E 523 MET cc_start: 0.7572 (tpp) cc_final: 0.7238 (tpt) REVERT: E 720 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6510 (pp) REVERT: E 819 LYS cc_start: 0.5296 (OUTLIER) cc_final: 0.4872 (pttm) REVERT: E 938 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5460 (pp) REVERT: F 457 ILE cc_start: 0.7270 (mm) cc_final: 0.6867 (pt) REVERT: F 565 ARG cc_start: 0.2139 (pmt170) cc_final: 0.1379 (mpt180) REVERT: F 659 TYR cc_start: 0.5556 (t80) cc_final: 0.5084 (m-80) REVERT: F 686 MET cc_start: -0.0190 (pmm) cc_final: -0.1475 (ptm) outliers start: 47 outliers final: 32 residues processed: 212 average time/residue: 0.3408 time to fit residues: 118.2101 Evaluate side-chains 209 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 833 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 20.0000 chunk 288 optimal weight: 0.8980 chunk 262 optimal weight: 9.9990 chunk 280 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 253 optimal weight: 0.4980 chunk 265 optimal weight: 20.0000 chunk 279 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 883 ASN ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25837 Z= 0.157 Angle : 0.584 14.161 35025 Z= 0.280 Chirality : 0.041 0.284 3949 Planarity : 0.004 0.074 4490 Dihedral : 7.366 123.276 3582 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.24 % Favored : 93.60 % Rotamer: Outliers : 1.58 % Allowed : 16.26 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.24 (0.16), residues: 3110 helix: 1.20 (0.15), residues: 1431 sheet: 0.76 (0.29), residues: 354 loop : -1.17 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 615 HIS 0.005 0.000 HIS F 863 PHE 0.012 0.001 PHE F 452 TYR 0.017 0.001 TYR F 823 ARG 0.014 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8311 (pp) REVERT: A 634 TYR cc_start: 0.4307 (m-10) cc_final: 0.3994 (m-80) REVERT: A 1375 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.5551 (pp) REVERT: A 1379 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7163 (mtm) REVERT: B 651 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7755 (tp) REVERT: E 720 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6510 (pp) REVERT: E 819 LYS cc_start: 0.5227 (OUTLIER) cc_final: 0.4813 (pttm) REVERT: E 938 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5608 (pp) REVERT: F 457 ILE cc_start: 0.7326 (mm) cc_final: 0.6926 (pt) REVERT: F 565 ARG cc_start: 0.2153 (pmt170) cc_final: 0.1372 (mpt180) REVERT: F 659 TYR cc_start: 0.5595 (t80) cc_final: 0.5077 (m-80) REVERT: F 686 MET cc_start: -0.0049 (pmm) cc_final: -0.1477 (ptm) outliers start: 44 outliers final: 32 residues processed: 208 average time/residue: 0.3343 time to fit residues: 113.9709 Evaluate side-chains 208 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 681 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 3.9990 chunk 296 optimal weight: 0.7980 chunk 180 optimal weight: 0.0870 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 chunk 247 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25837 Z= 0.156 Angle : 0.592 15.476 35025 Z= 0.282 Chirality : 0.041 0.245 3949 Planarity : 0.004 0.057 4490 Dihedral : 7.198 110.177 3582 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 1.51 % Allowed : 16.41 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.30 (0.16), residues: 3110 helix: 1.25 (0.15), residues: 1432 sheet: 0.79 (0.29), residues: 361 loop : -1.16 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 615 HIS 0.005 0.000 HIS F 863 PHE 0.012 0.001 PHE F 452 TYR 0.016 0.001 TYR F 823 ARG 0.009 0.000 ARG A 576 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8307 (pp) REVERT: A 576 ARG cc_start: 0.6755 (ttp-110) cc_final: 0.6258 (mtm110) REVERT: A 1375 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.5522 (pp) REVERT: A 1379 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7174 (mtm) REVERT: B 651 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7760 (tp) REVERT: E 720 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6506 (pp) REVERT: E 819 LYS cc_start: 0.5247 (OUTLIER) cc_final: 0.4831 (pttm) REVERT: E 938 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5231 (pt) REVERT: F 457 ILE cc_start: 0.7329 (mm) cc_final: 0.6927 (pt) REVERT: F 565 ARG cc_start: 0.2164 (pmt170) cc_final: 0.1376 (mpt180) REVERT: F 659 TYR cc_start: 0.5613 (t80) cc_final: 0.5146 (m-80) REVERT: F 686 MET cc_start: -0.0313 (pmm) cc_final: -0.1485 (ptm) outliers start: 42 outliers final: 33 residues processed: 209 average time/residue: 0.3319 time to fit residues: 114.3990 Evaluate side-chains 209 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 681 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1354 ASN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1330 HIS ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.104323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072517 restraints weight = 87978.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073692 restraints weight = 51583.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073944 restraints weight = 40155.587| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25837 Z= 0.269 Angle : 0.652 15.345 35025 Z= 0.317 Chirality : 0.042 0.243 3949 Planarity : 0.004 0.077 4490 Dihedral : 7.430 98.200 3582 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.04 % Favored : 92.80 % Rotamer: Outliers : 1.69 % Allowed : 16.62 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.22 (0.16), residues: 3110 helix: 1.22 (0.15), residues: 1431 sheet: 0.54 (0.28), residues: 370 loop : -1.19 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 866 HIS 0.005 0.001 HIS F 863 PHE 0.014 0.001 PHE E 517 TYR 0.019 0.001 TYR A 823 ARG 0.018 0.001 ARG B 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.54 seconds wall clock time: 77 minutes 7.95 seconds (4627.95 seconds total)