Starting phenix.real_space_refine on Fri Apr 12 09:05:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/04_2024/8juw_36665_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/04_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_36665/04_2024/8juw_36665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/04_2024/8juw_36665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/04_2024/8juw_36665_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juw_36665/04_2024/8juw_36665_neut_updated.pdb" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 13.24, per 1000 atoms: 0.52 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: 11.42 Conformation dependent library (CDL) restraints added in 4.3 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... running ksdssp... Secondary structure from input PDB file: 154 helices and 13 sheets defined 44.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 433 through 447 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 475 through 484 Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 601 through 611 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 637 through 654 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 678 through 684 Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 706 through 720 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) Processing helix chain 'A' and resid 725 through 728 removed outlier: 4.023A pdb=" N GLU A 728 " --> pdb=" O PRO A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 725 through 728' Processing helix chain 'A' and resid 809 through 816 Processing helix chain 'A' and resid 827 through 830 No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing helix chain 'A' and resid 838 through 851 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) Processing helix chain 'A' and resid 862 through 867 removed outlier: 4.945A pdb=" N GLU A 867 " --> pdb=" O HIS A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 905 through 910 removed outlier: 4.190A pdb=" N LEU A 910 " --> pdb=" O GLU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 926 through 937 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 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 1332 through 1344 Processing helix chain 'A' and resid 1349 through 1366 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) removed outlier: 3.656A pdb=" N HIS A1366 " --> pdb=" O CYS A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1385 removed outlier: 4.814A pdb=" N GLU A1384 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 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 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.511A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 455' Processing helix chain 'B' and resid 473 through 484 removed outlier: 4.295A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 522 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) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 546 through 559 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 601 through 611 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 621 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 637 through 645 removed outlier: 3.781A pdb=" N ALA B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 676 through 685 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 706 through 723 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 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 809 through 816 Processing helix chain 'B' and resid 827 through 830 No H-bonds generated for 'chain 'B' and resid 827 through 830' Processing helix chain 'B' and resid 838 through 851 Processing helix chain 'B' and resid 862 through 868 removed outlier: 5.065A pdb=" N GLU B 867 " --> pdb=" O HIS B 863 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 868 " --> pdb=" O VAL B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 881 Processing helix chain 'B' and resid 900 through 902 No H-bonds generated for 'chain 'B' and resid 900 through 902' Processing helix chain 'B' and resid 905 through 910 removed outlier: 4.171A pdb=" N LEU B 910 " --> pdb=" O GLU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 926 through 932 Processing helix chain 'B' and resid 1332 through 1343 Processing helix chain 'B' and resid 1349 through 1366 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) removed outlier: 3.857A pdb=" N HIS B1366 " --> pdb=" O CYS B1362 " (cutoff:3.500A) Processing helix chain 'B' and resid 1376 through 1385 removed outlier: 3.533A pdb=" N GLU B1384 " --> pdb=" O GLU B1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 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 444 through 447 No H-bonds generated for 'chain 'C' and resid 444 through 447' Processing helix chain 'C' and resid 452 through 455 No H-bonds generated for 'chain 'C' and resid 452 through 455' Processing helix chain 'C' and resid 474 through 485 Processing helix chain 'C' and resid 511 through 523 Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 547 through 558 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 582 through 584 No H-bonds generated for 'chain 'C' and resid 582 through 584' Processing helix chain 'C' and resid 601 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 621 through 630 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) Processing helix chain 'C' and resid 636 through 654 removed outlier: 3.916A pdb=" N CYS C 643 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA C 646 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 684 Processing helix chain 'C' and resid 706 through 708 No H-bonds generated for 'chain 'C' and resid 706 through 708' Processing helix chain 'C' and resid 710 through 723 Processing helix chain 'C' and resid 810 through 816 Processing helix chain 'C' and resid 827 through 830 No H-bonds generated for 'chain 'C' and resid 827 through 830' Processing helix chain 'C' and resid 838 through 851 removed outlier: 3.881A pdb=" N ILE C 846 " --> pdb=" O CYS C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 865 No H-bonds generated for 'chain 'C' and resid 862 through 865' Processing helix chain 'C' and resid 871 through 880 Processing helix chain 'C' and resid 900 through 902 No H-bonds generated for 'chain 'C' and resid 900 through 902' Processing helix chain 'C' and resid 913 through 915 No H-bonds generated for 'chain 'C' and resid 913 through 915' Processing helix chain 'C' and resid 926 through 938 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 1332 through 1343 Processing helix chain 'C' and resid 1349 through 1365 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 1384 Processing helix chain 'D' and resid 433 through 442 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 444 through 447 No H-bonds generated for 'chain 'D' and resid 444 through 447' Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.386A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 451 through 455' Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.781A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 522 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 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 547 through 559 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) Processing helix chain 'D' and resid 601 through 611 removed outlier: 5.504A pdb=" N LYS D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 removed outlier: 3.871A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 654 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 658 No H-bonds generated for 'chain 'D' and resid 656 through 658' Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.577A pdb=" N GLN D 684 " --> pdb=" O GLU D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 692 No H-bonds generated for 'chain 'D' and resid 690 through 692' Processing helix chain 'D' and resid 703 through 723 Proline residue: D 707 - end of helix 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 810 through 816 Processing helix chain 'D' and resid 827 through 832 removed outlier: 3.729A pdb=" N GLY D 832 " --> pdb=" O PRO D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 851 removed outlier: 3.798A pdb=" N ILE D 846 " --> pdb=" O CYS D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 867 removed outlier: 5.105A pdb=" N GLU D 867 " --> pdb=" O HIS D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 880 Processing helix chain 'D' and resid 900 through 902 No H-bonds generated for 'chain 'D' and resid 900 through 902' Processing helix chain 'D' and resid 905 through 909 Processing helix chain 'D' and resid 913 through 915 No H-bonds generated for 'chain 'D' and resid 913 through 915' Processing helix chain 'D' and resid 926 through 937 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 1332 through 1343 Processing helix chain 'D' and resid 1349 through 1365 removed outlier: 3.530A pdb=" N CYS D1362 " --> pdb=" O VAL D1358 " (cutoff:3.500A) Processing helix chain 'D' and resid 1376 through 1385 Processing helix chain 'E' and resid 436 through 442 removed outlier: 3.748A pdb=" N MET E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 447 No H-bonds generated for 'chain 'E' and resid 444 through 447' Processing helix chain 'E' and resid 451 through 454 No H-bonds generated for 'chain 'E' and resid 451 through 454' Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 511 through 523 Processing helix chain 'E' and resid 533 through 535 No H-bonds generated for 'chain 'E' and resid 533 through 535' Processing helix chain 'E' and resid 546 through 560 removed outlier: 3.830A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 611 Processing helix chain 'E' and resid 621 through 630 removed outlier: 4.091A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 654 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 676 through 685 removed outlier: 3.508A pdb=" N LYS E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 723 Proline residue: E 707 - end of helix 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 809 through 816 Processing helix chain 'E' and resid 827 through 830 No H-bonds generated for 'chain 'E' and resid 827 through 830' Processing helix chain 'E' and resid 838 through 851 Processing helix chain 'E' and resid 862 through 865 No H-bonds generated for 'chain 'E' and resid 862 through 865' Processing helix chain 'E' and resid 871 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 905 through 910 removed outlier: 3.782A pdb=" N GLU E 909 " --> pdb=" O GLU E 905 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU E 910 " --> pdb=" O GLU E 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 905 through 910' Processing helix chain 'E' and resid 913 through 915 No H-bonds generated for 'chain 'E' and resid 913 through 915' Processing helix chain 'E' and resid 926 through 932 Processing helix chain 'E' and resid 936 through 939 No H-bonds generated for 'chain 'E' and resid 936 through 939' Processing helix chain 'E' and resid 1331 through 1343 Processing helix chain 'E' and resid 1349 through 1366 removed outlier: 3.641A pdb=" N HIS E1366 " --> pdb=" O CYS E1362 " (cutoff:3.500A) Processing helix chain 'E' and resid 1376 through 1385 Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.974A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 447 Processing helix chain 'F' and resid 449 through 452 No H-bonds generated for 'chain 'F' and resid 449 through 452' Processing helix chain 'F' and resid 473 through 485 removed outlier: 3.601A pdb=" N ALA F 477 " --> pdb=" O LYS F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 522 removed outlier: 3.893A pdb=" N TYR F 521 " --> pdb=" O PHE F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 536 No H-bonds generated for 'chain 'F' and resid 533 through 536' Processing helix chain 'F' and resid 546 through 561 Processing helix chain 'F' and resid 602 through 611 removed outlier: 4.181A pdb=" N GLU F 606 " --> pdb=" O GLU F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 630 Processing helix chain 'F' and resid 637 through 653 removed outlier: 3.591A pdb=" N CYS F 643 " --> pdb=" O ILE F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 658 No H-bonds generated for 'chain 'F' and resid 656 through 658' Processing helix chain 'F' and resid 676 through 685 removed outlier: 4.055A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS F 685 " --> pdb=" O VAL F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 723 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 809 through 816 Processing helix chain 'F' and resid 827 through 830 No H-bonds generated for 'chain 'F' and resid 827 through 830' Processing helix chain 'F' and resid 838 through 851 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 862 through 867 removed outlier: 4.920A pdb=" N GLU F 867 " --> pdb=" O HIS F 863 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 882 removed outlier: 3.866A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 900 through 902 No H-bonds generated for 'chain 'F' and resid 900 through 902' Processing helix chain 'F' and resid 905 through 910 removed outlier: 3.779A pdb=" N LEU F 910 " --> pdb=" O GLU F 906 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 933 removed outlier: 4.030A pdb=" N PHE F 933 " --> pdb=" O ARG F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 1333 through 1346 removed outlier: 3.898A pdb=" N GLN F1345 " --> pdb=" O VAL F1341 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASN F1346 " --> pdb=" O LYS F1342 " (cutoff:3.500A) Processing helix chain 'F' and resid 1349 through 1365 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 1375 through 1385 removed outlier: 3.522A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 592 through 595 removed outlier: 3.834A pdb=" N ARG A 592 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N CYS A 463 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 570 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE A 465 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 572 " --> pdb=" O PHE A 465 " (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: 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) Processing sheet with id= B, first strand: chain 'A' and resid 918 through 920 removed outlier: 8.194A pdb=" N PHE A 919 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 796 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ILE A 795 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 892 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE A 797 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA A 894 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 855 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 893 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 857 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 895 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL A 859 " --> pdb=" O THR A 895 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 464 through 467 Processing sheet with id= D, first strand: chain 'B' and resid 494 through 496 Processing sheet with id= E, first strand: chain 'B' and resid 918 through 920 removed outlier: 8.371A pdb=" N PHE B 919 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 796 " --> pdb=" O PHE B 919 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE B 795 " --> pdb=" O VAL B 890 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 892 " --> pdb=" O ILE B 795 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE B 797 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 894 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER B 855 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU B 893 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 857 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR B 895 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL B 859 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 592 through 596 removed outlier: 8.546A pdb=" N CYS C 463 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 570 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE C 465 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY C 572 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY C 467 " --> pdb=" O GLY C 572 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR C 574 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER C 526 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ILE C 571 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 528 " --> pdb=" O ILE C 571 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ALA C 573 " --> pdb=" O ILE C 528 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE C 530 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE C 494 " --> pdb=" O PHE C 529 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP C 531 " --> pdb=" O PHE C 494 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG C 496 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 794 through 797 removed outlier: 8.437A pdb=" N ILE C 795 " --> pdb=" O VAL C 890 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 892 " --> pdb=" O ILE C 795 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE C 797 " --> pdb=" O LEU C 892 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA C 894 " --> pdb=" O ILE C 797 " (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: 6.832A pdb=" N THR C 821 " --> pdb=" O ILE C 856 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR C 858 " --> pdb=" O THR C 821 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR C 823 " --> pdb=" O TYR C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 593 through 596 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) removed outlier: 7.426A pdb=" N PHE D 596 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR D 466 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N CYS D 463 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 570 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N PHE D 465 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY D 572 " --> pdb=" O PHE D 465 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N GLY D 467 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER D 526 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE D 571 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE D 528 " --> pdb=" O ILE D 571 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA D 573 " --> pdb=" O ILE D 528 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE D 530 " --> pdb=" O ALA D 573 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 918 through 920 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) removed outlier: 8.350A pdb=" N ILE D 795 " --> pdb=" O VAL D 890 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 892 " --> pdb=" O ILE D 795 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE D 797 " --> pdb=" O LEU D 892 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA D 894 " --> pdb=" O ILE D 797 " (cutoff:3.500A) 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: 6.832A pdb=" N THR D 821 " --> pdb=" O ILE D 856 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR D 858 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR D 823 " --> pdb=" O TYR D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 592 through 595 removed outlier: 8.950A pdb=" N CYS E 463 " --> pdb=" O ILE E 568 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL E 570 " --> pdb=" O CYS E 463 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE E 465 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY E 572 " --> pdb=" O PHE E 465 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER E 526 " --> pdb=" O VAL E 569 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ILE E 571 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE E 528 " --> pdb=" O ILE E 571 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA E 573 " --> pdb=" O ILE E 528 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE E 530 " --> pdb=" O ALA E 573 " (cutoff:3.500A) 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) Processing sheet with id= K, first strand: chain 'E' and resid 918 through 920 removed outlier: 8.575A pdb=" N PHE E 919 " --> pdb=" O ARG E 794 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU E 796 " --> pdb=" O PHE E 919 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE E 795 " --> pdb=" O VAL E 890 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU E 892 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE E 797 " --> pdb=" O LEU E 892 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA E 894 " --> pdb=" O ILE E 797 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER E 855 " --> pdb=" O LEU E 891 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU E 893 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL E 857 " --> pdb=" O LEU E 893 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR E 895 " --> pdb=" O VAL E 857 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL E 859 " --> pdb=" O THR E 895 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 594 through 596 removed outlier: 7.951A pdb=" N CYS F 463 " --> pdb=" O ILE F 568 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL F 570 " --> pdb=" O CYS F 463 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE F 465 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY F 572 " --> pdb=" O PHE F 465 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLY F 467 " --> pdb=" O GLY F 572 " (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) 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) Processing sheet with id= M, first strand: chain 'F' and resid 918 through 920 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) removed outlier: 6.289A pdb=" N LEU F 892 " --> pdb=" O ILE F 795 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE F 797 " --> pdb=" O LEU F 892 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA F 894 " --> pdb=" O ILE F 797 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR F 895 " --> pdb=" O VAL F 859 " (cutoff:3.500A) 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) 729 hydrogen bonds defined for protein. 2130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.88 Time building geometry restraints manager: 11.85 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: 410 2.66 - 3.22: 24479 3.22 - 3.78: 35834 3.78 - 4.34: 47262 4.34 - 4.90: 77685 Nonbonded interactions: 185670 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 185665 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.710 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 68.640 Find NCS groups from input model: 2.240 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.200 ------------------------------------------------------------------------------- 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= 0.414 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 : 2.965 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: 0.4816 time to fit residues: 294.7698 Evaluate side-chains 186 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.978 ------------------------------------------------------------------------------- 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: 8.9990 chunk 236 optimal weight: 0.2980 chunk 131 optimal weight: 0.0470 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 283 optimal weight: 6.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25837 Z= 0.185 Angle : 0.634 10.968 35025 Z= 0.312 Chirality : 0.043 0.176 3949 Planarity : 0.005 0.056 4490 Dihedral : 9.500 174.038 3582 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 1.08 % Allowed : 9.25 % Favored : 89.67 % 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: 1395 sheet: 0.13 (0.28), residues: 375 loop : -1.44 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 865 HIS 0.007 0.001 HIS B 611 PHE 0.018 0.001 PHE F 465 TYR 0.019 0.001 TYR A 858 ARG 0.007 0.000 ARG E 913 *********************** 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 261 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ARG cc_start: 0.6508 (ttp-110) cc_final: 0.6224 (mtm110) REVERT: A 615 TRP cc_start: 0.4510 (m-10) cc_final: 0.3988 (m100) REVERT: E 546 GLN cc_start: 0.8342 (pp30) cc_final: 0.8089 (pt0) REVERT: F 441 MET cc_start: 0.4609 (ptm) cc_final: 0.4367 (ptt) REVERT: F 457 ILE cc_start: 0.7113 (mm) cc_final: 0.6743 (pt) REVERT: F 565 ARG cc_start: 0.2258 (pmt170) cc_final: 0.1675 (mpt180) REVERT: F 638 ASP cc_start: 0.4652 (p0) cc_final: 0.4342 (m-30) REVERT: F 686 MET cc_start: -0.0235 (pmm) cc_final: -0.1588 (ptm) outliers start: 30 outliers final: 14 residues processed: 250 average time/residue: 0.3818 time to fit residues: 150.6337 Evaluate side-chains 200 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain B residue 484 CYS 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 613 ARG 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 Chi-restraints excluded: chain F residue 892 LEU 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: 6.9990 chunk 192 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 283 optimal weight: 9.9990 chunk 306 optimal weight: 0.0010 chunk 252 optimal weight: 9.9990 chunk 281 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 overall best weight: 3.1392 ------------------------------------------------------------------------------- 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** ** E 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25837 Z= 0.363 Angle : 0.697 10.774 35025 Z= 0.346 Chirality : 0.044 0.159 3949 Planarity : 0.005 0.064 4490 Dihedral : 9.327 179.313 3582 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.62 % Favored : 92.22 % Rotamer: Outliers : 2.16 % Allowed : 11.80 % Favored : 86.04 % 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: -0.68 (0.15), residues: 3110 helix: 0.42 (0.14), residues: 1384 sheet: 0.01 (0.28), residues: 371 loop : -1.48 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 866 HIS 0.006 0.001 HIS A 815 PHE 0.018 0.002 PHE F 465 TYR 0.017 0.002 TYR A 858 ARG 0.008 0.001 ARG C1367 *********************** 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 246 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 186 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 TRP cc_start: 0.5013 (m-10) cc_final: 0.4289 (m100) REVERT: D 717 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8532 (mm) REVERT: E 938 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5481 (pp) REVERT: F 457 ILE cc_start: 0.7348 (mm) cc_final: 0.6981 (pt) REVERT: F 686 MET cc_start: -0.0005 (pmm) cc_final: -0.1409 (ptm) outliers start: 60 outliers final: 32 residues processed: 230 average time/residue: 0.3731 time to fit residues: 137.2801 Evaluate side-chains 190 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL 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 B residue 518 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain C residue 614 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 937 ILE 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 517 PHE Chi-restraints excluded: chain E residue 635 CYS 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 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 Chi-restraints excluded: chain F residue 709 LEU 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: 0.0270 chunk 147 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 269 optimal weight: 30.0000 chunk 81 optimal weight: 0.8980 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1381 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 908 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25837 Z= 0.176 Angle : 0.573 10.153 35025 Z= 0.278 Chirality : 0.041 0.132 3949 Planarity : 0.004 0.050 4490 Dihedral : 8.844 174.975 3582 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.14 % Favored : 93.76 % Rotamer: Outliers : 1.73 % Allowed : 13.67 % Favored : 84.60 % 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: -0.40 (0.16), residues: 3110 helix: 0.69 (0.15), residues: 1386 sheet: 0.27 (0.28), residues: 380 loop : -1.43 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 865 HIS 0.003 0.001 HIS A 815 PHE 0.029 0.001 PHE C 455 TYR 0.018 0.001 TYR A 448 ARG 0.010 0.000 ARG B 543 *********************** 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 230 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8435 (pp) REVERT: A 576 ARG cc_start: 0.6755 (ttp-110) cc_final: 0.6359 (mtm110) REVERT: A 615 TRP cc_start: 0.4952 (m-10) cc_final: 0.4303 (m100) REVERT: A 1375 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6243 (pp) REVERT: D 717 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8421 (mm) REVERT: E 938 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5454 (pp) REVERT: F 457 ILE cc_start: 0.7294 (mm) cc_final: 0.6919 (pt) REVERT: F 565 ARG cc_start: 0.2170 (pmt170) cc_final: 0.1442 (mtt180) REVERT: F 686 MET cc_start: -0.0144 (pmm) cc_final: -0.1402 (ptm) outliers start: 48 outliers final: 30 residues processed: 219 average time/residue: 0.3556 time to fit residues: 126.7905 Evaluate side-chains 189 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 3.172 ------------------------------------------------------------------------------- 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 825 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 837 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 D residue 471 THR Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 631 CYS 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 648 LEU Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 720 LEU 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 709 LEU Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain F residue 892 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.0010 chunk 171 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 257 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25837 Z= 0.240 Angle : 0.587 11.173 35025 Z= 0.286 Chirality : 0.041 0.188 3949 Planarity : 0.004 0.050 4490 Dihedral : 8.576 174.274 3582 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 2.45 % Allowed : 14.47 % Favored : 83.09 % 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: -0.32 (0.16), residues: 3110 helix: 0.75 (0.15), residues: 1398 sheet: 0.27 (0.28), residues: 376 loop : -1.39 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 865 HIS 0.003 0.001 HIS D 434 PHE 0.018 0.001 PHE F 465 TYR 0.016 0.001 TYR F 659 ARG 0.005 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 236 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 168 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 TRP cc_start: 0.5067 (m-10) cc_final: 0.4503 (m100) REVERT: A 1375 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6295 (pp) REVERT: B 686 MET cc_start: 0.7305 (tmm) cc_final: 0.7097 (tmm) REVERT: D 717 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8423 (mm) REVERT: E 938 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5508 (pp) REVERT: F 457 ILE cc_start: 0.7320 (mm) cc_final: 0.6949 (pt) REVERT: F 565 ARG cc_start: 0.1548 (pmt170) cc_final: 0.0755 (mtt90) REVERT: F 686 MET cc_start: -0.0033 (pmm) cc_final: -0.1283 (ptm) outliers start: 68 outliers final: 47 residues processed: 220 average time/residue: 0.3547 time to fit residues: 126.5418 Evaluate side-chains 205 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 3.149 ------------------------------------------------------------------------------- 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 526 SER Chi-restraints excluded: chain A residue 559 MET 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 1375 LEU Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain C residue 614 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 D residue 471 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 624 LEU 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 709 LEU 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 423 VAL 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 649 CYS 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 E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 641 SER Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 833 VAL Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain F residue 892 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 4.9990 chunk 271 optimal weight: 8.9990 chunk 59 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 546 GLN F 900 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25837 Z= 0.239 Angle : 0.593 16.157 35025 Z= 0.288 Chirality : 0.041 0.184 3949 Planarity : 0.004 0.050 4490 Dihedral : 8.318 165.546 3582 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.78 % Favored : 93.09 % Rotamer: Outliers : 2.88 % Allowed : 15.15 % Favored : 81.97 % 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: -0.23 (0.16), residues: 3110 helix: 0.83 (0.15), residues: 1397 sheet: 0.34 (0.28), residues: 383 loop : -1.36 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 615 HIS 0.004 0.001 HIS B 548 PHE 0.018 0.001 PHE F 465 TYR 0.014 0.001 TYR A 448 ARG 0.007 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: 80 poor density : 160 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8451 (pp) REVERT: A 576 ARG cc_start: 0.6794 (ttp-110) cc_final: 0.6322 (mtm110) REVERT: A 634 TYR cc_start: 0.4241 (m-10) cc_final: 0.3648 (m-80) REVERT: A 819 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7299 (pttm) REVERT: A 1375 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6216 (pp) REVERT: C 708 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8287 (tt) REVERT: D 717 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8459 (mm) REVERT: E 546 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7474 (pp30) REVERT: E 638 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.6093 (m-30) REVERT: E 938 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5781 (pp) REVERT: F 457 ILE cc_start: 0.7400 (mm) cc_final: 0.6991 (pt) REVERT: F 686 MET cc_start: 0.0191 (pmm) cc_final: -0.1214 (ptm) outliers start: 80 outliers final: 58 residues processed: 223 average time/residue: 0.3449 time to fit residues: 127.4242 Evaluate side-chains 217 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 151 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL 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 526 SER Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 559 MET 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 717 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 1373 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 714 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 C residue 923 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 624 LEU 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 709 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 789 MET 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 423 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 484 CYS Chi-restraints excluded: chain E residue 517 PHE Chi-restraints excluded: chain E residue 546 GLN Chi-restraints excluded: chain E residue 638 ASP 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 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 681 VAL Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 833 VAL Chi-restraints excluded: chain F residue 864 VAL Chi-restraints excluded: chain F residue 892 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN E1385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25837 Z= 0.195 Angle : 0.580 15.329 35025 Z= 0.279 Chirality : 0.041 0.212 3949 Planarity : 0.004 0.055 4490 Dihedral : 8.057 152.125 3582 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.95 % Favored : 92.96 % Rotamer: Outliers : 2.30 % Allowed : 16.34 % Favored : 81.36 % 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: -0.12 (0.16), residues: 3110 helix: 0.89 (0.15), residues: 1397 sheet: 0.48 (0.28), residues: 375 loop : -1.29 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 615 HIS 0.006 0.001 HIS E 548 PHE 0.017 0.001 PHE F 465 TYR 0.019 0.001 TYR F 659 ARG 0.011 0.000 ARG B 543 *********************** 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 232 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 168 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8395 (pp) REVERT: A 576 ARG cc_start: 0.6738 (ttp-110) cc_final: 0.6382 (mtm110) REVERT: A 634 TYR cc_start: 0.4287 (m-10) cc_final: 0.3869 (m-80) REVERT: A 819 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7264 (pttm) REVERT: A 1375 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6180 (pp) REVERT: C 708 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8291 (tt) REVERT: D 717 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8438 (mm) REVERT: E 638 ASP cc_start: 0.6389 (OUTLIER) cc_final: 0.6070 (m-30) REVERT: E 938 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5776 (pp) REVERT: F 457 ILE cc_start: 0.7354 (mm) cc_final: 0.6943 (pt) REVERT: F 686 MET cc_start: 0.0176 (pmm) cc_final: -0.1233 (ptm) outliers start: 64 outliers final: 47 residues processed: 218 average time/residue: 0.3520 time to fit residues: 125.4852 Evaluate side-chains 206 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 152 time to evaluate : 3.026 ------------------------------------------------------------------------------- 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 458 GLN Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 526 SER 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 819 LYS Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 714 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 570 VAL Chi-restraints excluded: chain D residue 624 LEU 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 709 LEU 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 423 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 638 ASP 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 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 705 VAL Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 833 VAL Chi-restraints excluded: chain F residue 892 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS A 458 GLN B 684 GLN E 546 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25837 Z= 0.258 Angle : 0.612 14.513 35025 Z= 0.296 Chirality : 0.042 0.193 3949 Planarity : 0.004 0.050 4490 Dihedral : 7.967 137.739 3582 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.56 % Favored : 92.35 % Rotamer: Outliers : 2.70 % Allowed : 16.16 % Favored : 81.14 % 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: -0.17 (0.16), residues: 3110 helix: 0.85 (0.15), residues: 1401 sheet: 0.39 (0.28), residues: 383 loop : -1.32 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 865 HIS 0.004 0.001 HIS F 863 PHE 0.018 0.001 PHE F 465 TYR 0.013 0.001 TYR A 915 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 226 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 151 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8441 (pp) REVERT: A 576 ARG cc_start: 0.6601 (ttp-110) cc_final: 0.6267 (mtm110) REVERT: A 819 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7297 (pttm) REVERT: A 1375 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6144 (pp) REVERT: C 708 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8329 (tt) REVERT: D 717 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8453 (mm) REVERT: E 546 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7633 (pp30) REVERT: E 638 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6170 (m-30) REVERT: E 938 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5921 (pp) REVERT: F 457 ILE cc_start: 0.7346 (mm) cc_final: 0.6970 (pt) REVERT: F 686 MET cc_start: 0.0281 (pmm) cc_final: -0.1072 (ptm) REVERT: F 1379 MET cc_start: 0.6309 (mmt) cc_final: 0.6095 (mmt) outliers start: 75 outliers final: 54 residues processed: 210 average time/residue: 0.3509 time to fit residues: 121.0409 Evaluate side-chains 210 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 148 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL 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 526 SER 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 717 LEU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 714 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 C residue 923 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 624 LEU 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 709 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 789 MET 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 423 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 484 CYS Chi-restraints excluded: chain E residue 546 GLN Chi-restraints excluded: chain E residue 638 ASP 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 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 709 LEU 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: 0.0020 chunk 262 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 220 optimal weight: 0.3980 chunk 85 optimal weight: 0.3980 chunk 253 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A1354 ASN E 546 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25837 Z= 0.158 Angle : 0.590 16.005 35025 Z= 0.284 Chirality : 0.041 0.192 3949 Planarity : 0.004 0.062 4490 Dihedral : 7.691 127.878 3582 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.31 % Rotamer: Outliers : 2.16 % Allowed : 16.91 % Favored : 80.93 % 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: -0.00 (0.16), residues: 3110 helix: 0.99 (0.15), residues: 1398 sheet: 0.59 (0.29), residues: 378 loop : -1.25 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 615 HIS 0.005 0.000 HIS F 863 PHE 0.015 0.001 PHE F 465 TYR 0.015 0.001 TYR F 659 ARG 0.013 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 228 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 168 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8389 (pp) REVERT: A 576 ARG cc_start: 0.6591 (ttp-110) cc_final: 0.6226 (mtm110) REVERT: A 1375 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6124 (pp) REVERT: D 717 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8441 (mm) REVERT: E 546 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7750 (pp30) REVERT: E 638 ASP cc_start: 0.6428 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: E 938 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5824 (pp) REVERT: F 457 ILE cc_start: 0.7253 (mm) cc_final: 0.6857 (pt) REVERT: F 524 ARG cc_start: 0.6848 (ptp90) cc_final: 0.6260 (ptm-80) REVERT: F 686 MET cc_start: 0.0234 (pmm) cc_final: -0.1160 (ptm) outliers start: 60 outliers final: 47 residues processed: 210 average time/residue: 0.3393 time to fit residues: 117.6537 Evaluate side-chains 205 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 152 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL 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 526 SER 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 717 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 475 LEU 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 822 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 714 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 570 VAL Chi-restraints excluded: chain D residue 624 LEU 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 709 LEU 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 423 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 546 GLN Chi-restraints excluded: chain E residue 638 ASP Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 720 LEU 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 495 MET Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 833 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: 4.9990 chunk 180 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 286 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A1354 ASN E 546 GLN E1366 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25837 Z= 0.198 Angle : 0.600 15.359 35025 Z= 0.287 Chirality : 0.041 0.247 3949 Planarity : 0.004 0.049 4490 Dihedral : 7.614 118.677 3582 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.01 % Favored : 92.89 % Rotamer: Outliers : 2.12 % Allowed : 17.13 % Favored : 80.75 % 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: 0.01 (0.16), residues: 3110 helix: 1.00 (0.15), residues: 1399 sheet: 0.57 (0.28), residues: 382 loop : -1.25 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 615 HIS 0.005 0.001 HIS F 863 PHE 0.018 0.001 PHE A 452 TYR 0.016 0.001 TYR A 448 ARG 0.009 0.000 ARG B 543 ********************** 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 216 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 157 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8396 (pp) REVERT: A 576 ARG cc_start: 0.6623 (ttp-110) cc_final: 0.6264 (mtm110) REVERT: A 634 TYR cc_start: 0.4371 (m-10) cc_final: 0.4072 (m-80) REVERT: A 1375 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6124 (pp) REVERT: E 638 ASP cc_start: 0.6412 (OUTLIER) cc_final: 0.6129 (m-30) REVERT: E 938 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5792 (pp) REVERT: F 457 ILE cc_start: 0.7275 (mm) cc_final: 0.6870 (pt) REVERT: F 524 ARG cc_start: 0.6919 (ptp90) cc_final: 0.6337 (ptm-80) REVERT: F 686 MET cc_start: 0.0273 (pmm) cc_final: -0.1126 (ptm) outliers start: 59 outliers final: 49 residues processed: 198 average time/residue: 0.3500 time to fit residues: 114.8270 Evaluate side-chains 205 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 152 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 526 SER 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 717 LEU Chi-restraints excluded: chain A residue 1375 LEU 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 822 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 714 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 570 VAL Chi-restraints excluded: chain D residue 624 LEU 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 709 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 423 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 484 CYS Chi-restraints excluded: chain E residue 638 ASP 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 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 672 ILE Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 75 optimal weight: 0.2980 chunk 228 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 0.0010 chunk 247 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.105267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074015 restraints weight = 87455.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075696 restraints weight = 51887.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075539 restraints weight = 37619.280| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25837 Z= 0.155 Angle : 0.589 15.411 35025 Z= 0.280 Chirality : 0.041 0.250 3949 Planarity : 0.004 0.049 4490 Dihedral : 7.427 110.006 3582 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.40 % Favored : 93.50 % Rotamer: Outliers : 1.76 % Allowed : 17.42 % Favored : 80.82 % 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: 0.11 (0.16), residues: 3110 helix: 1.08 (0.15), residues: 1396 sheet: 0.73 (0.29), residues: 377 loop : -1.21 (0.18), residues: 1337 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 0.015 0.001 PHE F 465 TYR 0.018 0.001 TYR F 659 ARG 0.009 0.000 ARG B 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4248.93 seconds wall clock time: 79 minutes 29.11 seconds (4769.11 seconds total)