Starting phenix.real_space_refine on Tue Mar 19 15:17:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/03_2024/8juy_36666_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/03_2024/8juy_36666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/03_2024/8juy_36666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/03_2024/8juy_36666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/03_2024/8juy_36666_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8juy_36666/03_2024/8juy_36666_neut_updated.pdb" } resolution = 4.34 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= 0.001 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 107 5.16 5 C 15675 2.51 5 N 4234 2.21 5 O 4521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 415": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 840": "OE1" <-> "OE2" Residue "B GLU 867": "OE1" <-> "OE2" Residue "B GLU 905": "OE1" <-> "OE2" Residue "B PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 934": "OE1" <-> "OE2" Residue "C PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 545": "OD1" <-> "OD2" Residue "C ASP 581": "OD1" <-> "OD2" Residue "C TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1371": "OD1" <-> "OD2" Residue "D ASP 420": "OD1" <-> "OD2" Residue "D ASP 426": "OD1" <-> "OD2" Residue "D PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 534": "OD1" <-> "OD2" Residue "D ASP 600": "OD1" <-> "OD2" Residue "D GLU 602": "OE1" <-> "OE2" Residue "D GLU 663": "OE1" <-> "OE2" Residue "D GLU 680": "OE1" <-> "OE2" Residue "D GLU 718": "OE1" <-> "OE2" Residue "D GLU 840": "OE1" <-> "OE2" Residue "D GLU 848": "OE1" <-> "OE2" Residue "D PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 518": "OD1" <-> "OD2" Residue "E PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 714": "OD1" <-> "OD2" Residue "E GLU 728": "OE1" <-> "OE2" Residue "E TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 510": "OE1" <-> "OE2" Residue "F PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 606": "OE1" <-> "OE2" Residue "F TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 668": "OD1" <-> "OD2" Residue "F GLU 905": "OE1" <-> "OE2" Residue "F PHE 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1369": "OD1" <-> "OD2" Residue "F GLU 1384": "OE1" <-> "OE2" Residue "F PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24554 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 406} Chain breaks: 3 Chain: "B" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4197 Classifications: {'peptide': 527} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 489} Chain breaks: 3 Chain: "C" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4190 Classifications: {'peptide': 527} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 492} Chain breaks: 3 Chain: "D" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4206 Classifications: {'peptide': 529} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 494} Chain breaks: 3 Chain: "E" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4188 Classifications: {'peptide': 526} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 489} Chain breaks: 3 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: 13.38, per 1000 atoms: 0.54 Number of scatterers: 24554 At special positions: 0 Unit cell: (141.9, 158.4, 139.7, 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 107 16.00 P 17 15.00 O 4521 8.00 N 4234 7.00 C 15675 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.18 Conformation dependent library (CDL) restraints added in 4.6 seconds 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 145 helices and 15 sheets defined 43.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.579A pdb=" N LEU A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.066A 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 483 Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 637 through 654 removed outlier: 3.791A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 706 through 721 removed outlier: 5.285A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) 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: 3.894A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 871 through 881 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: 4.178A 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 'B' and resid 433 through 447 removed outlier: 3.625A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 473 through 484 removed outlier: 4.150A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 509 No H-bonds generated for 'chain 'B' and resid 506 through 509' Processing helix chain 'B' and resid 511 through 522 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 removed outlier: 3.559A pdb=" N MET B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) 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 612 Processing helix chain 'B' and resid 621 through 630 removed outlier: 3.566A pdb=" N ASN B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 647 removed outlier: 3.624A pdb=" N ALA B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA B 647 " --> pdb=" O CYS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 676 through 685 removed outlier: 3.814A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 693 No H-bonds generated for 'chain 'B' and resid 690 through 693' Processing helix chain 'B' and resid 703 through 723 Proline residue: B 707 - end of helix removed outlier: 5.735A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.871A 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: 5.114A pdb=" N GLU B 867 " --> pdb=" O HIS B 863 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 868 " --> pdb=" O VAL B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 882 removed outlier: 3.878A pdb=" N LEU B 881 " --> pdb=" O PHE B 877 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) 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 908 No H-bonds generated for 'chain 'B' and resid 905 through 908' 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 934 Processing helix chain 'B' and resid 1332 through 1343 Processing helix chain 'B' and resid 1349 through 1364 removed outlier: 3.888A pdb=" N TYR B1356 " --> pdb=" O LEU B1352 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA B1357 " --> pdb=" O GLU B1353 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B1358 " --> pdb=" O ASN B1354 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B1360 " --> pdb=" O TYR B1356 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS B1362 " --> pdb=" O VAL B1358 " (cutoff:3.500A) Processing helix chain 'B' and resid 1376 through 1384 Processing helix chain 'C' and resid 433 through 442 removed outlier: 4.012A pdb=" N GLU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 4.293A 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 449 through 454 removed outlier: 4.498A pdb=" N GLU C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 454' Processing helix chain 'C' and resid 474 through 485 Processing helix chain 'C' and resid 506 through 509 No H-bonds generated for 'chain 'C' and resid 506 through 509' 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 546 through 559 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 601 through 612 Processing helix chain 'C' and resid 621 through 629 removed outlier: 4.240A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 654 removed outlier: 4.291A pdb=" N ALA C 646 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.728A pdb=" N TYR C 659 " --> pdb=" O PRO C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 685 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: 3.776A pdb=" N ILE C 846 " --> pdb=" O CYS C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 867 removed outlier: 4.886A pdb=" N GLU C 867 " --> pdb=" O HIS C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 880 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' 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: 3.598A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 4.901A 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: 3.556A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1375 through 1385 Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.799A pdb=" N GLU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (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 473 through 485 removed outlier: 3.677A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 522 removed outlier: 4.252A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (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 546 through 559 removed outlier: 3.776A pdb=" N SER D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 558 " --> pdb=" O THR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 584 No H-bonds generated for 'chain 'D' and resid 582 through 584' Processing helix chain 'D' and resid 601 through 612 removed outlier: 3.589A pdb=" N THR D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 removed outlier: 3.886A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 654 removed outlier: 3.646A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 4.045A 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 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 706 through 723 removed outlier: 6.089A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.819A 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: 3.576A pdb=" N GLY D 832 " --> pdb=" O PRO D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 851 Processing helix chain 'D' and resid 862 through 868 removed outlier: 5.287A pdb=" N GLU D 867 " --> pdb=" O HIS D 863 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 868 " --> pdb=" O VAL D 864 " (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: 4.561A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1333 through 1343 Processing helix chain 'D' and resid 1349 through 1365 Processing helix chain 'D' and resid 1376 through 1385 Processing helix chain 'E' and resid 434 through 447 removed outlier: 3.840A pdb=" N MET E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Proline residue: E 445 - end of helix 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 506 through 522 removed outlier: 4.405A pdb=" N GLU E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) 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 564 removed outlier: 3.708A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP E 563 " --> pdb=" O MET E 559 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER E 564 " --> pdb=" O ASP E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 611 Processing helix chain 'E' and resid 621 through 630 removed outlier: 4.293A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 654 removed outlier: 3.640A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 685 Processing helix chain 'E' and resid 703 through 721 Proline residue: E 707 - end of helix removed outlier: 6.228A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 801 through 803 No H-bonds generated for 'chain 'E' and resid 801 through 803' 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 880 Processing helix chain 'E' and resid 905 through 910 removed outlier: 3.761A pdb=" N GLU E 909 " --> pdb=" O GLU E 905 " (cutoff:3.500A) removed outlier: 6.084A 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 934 Processing helix chain 'E' and resid 940 through 942 No H-bonds generated for 'chain 'E' and resid 940 through 942' Processing helix chain 'E' and resid 1331 through 1343 Processing helix chain 'E' and resid 1349 through 1366 Processing helix chain 'E' and resid 1376 through 1384 Processing helix chain 'F' and resid 432 through 440 removed outlier: 3.527A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA F 437 " --> pdb=" O ASN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 484 Processing helix chain 'F' and resid 508 through 522 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 removed outlier: 4.367A pdb=" N ASP F 560 " --> pdb=" O LEU F 556 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 579 No H-bonds generated for 'chain 'F' and resid 577 through 579' Processing helix chain 'F' and resid 602 through 611 removed outlier: 4.173A 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 638 through 653 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 677 through 680 No H-bonds generated for 'chain 'F' and resid 677 through 680' Processing helix chain 'F' and resid 683 through 685 No H-bonds generated for 'chain 'F' and resid 683 through 685' Processing helix chain 'F' and resid 706 through 723 removed outlier: 5.913A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 815 Processing helix chain 'F' and resid 841 through 851 removed outlier: 3.791A pdb=" N ILE F 846 " --> pdb=" O CYS F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 862 through 868 removed outlier: 5.118A pdb=" N GLU F 867 " --> pdb=" O HIS F 863 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE F 868 " --> pdb=" O VAL F 864 " (cutoff:3.500A) Processing helix chain 'F' and resid 872 through 882 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: 4.311A pdb=" N LEU F 910 " --> pdb=" O GLU F 906 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 933 Processing helix chain 'F' and resid 1332 through 1343 Processing helix chain 'F' and resid 1349 through 1366 removed outlier: 4.115A pdb=" N HIS F1366 " --> pdb=" O CYS F1362 " (cutoff:3.500A) Processing helix chain 'F' and resid 1375 through 1385 removed outlier: 3.513A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 462 through 464 removed outlier: 9.045A pdb=" N CYS A 463 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 570 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER A 526 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE A 571 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE A 528 " --> pdb=" O ILE A 571 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 796 through 798 removed outlier: 3.979A pdb=" N PHE A 919 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 822 through 824 removed outlier: 6.125A pdb=" N ILE A 856 " --> pdb=" O TYR A 823 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 891 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL A 859 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU A 893 " --> pdb=" O VAL A 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 593 through 596 removed outlier: 8.592A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE B 596 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR B 466 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 570 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE B 465 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 572 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLY B 467 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR B 574 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 573 " --> pdb=" O PHE B 530 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE B 494 " --> pdb=" O PHE B 529 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 796 through 799 Processing sheet with id= F, first strand: chain 'B' and resid 821 through 824 Processing sheet with id= G, first strand: chain 'C' and resid 592 through 595 removed outlier: 3.655A pdb=" N TYR C 466 " --> pdb=" O PHE C 594 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N CYS C 463 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 570 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE C 465 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY C 572 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER C 526 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ILE C 571 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 528 " --> pdb=" O ILE C 571 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA C 573 " --> pdb=" O ILE C 528 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE C 530 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE C 494 " --> pdb=" O PHE C 529 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 794 through 798 removed outlier: 7.961A pdb=" N ILE C 795 " --> pdb=" O VAL C 890 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU C 892 " --> pdb=" O ILE C 795 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE C 797 " --> pdb=" O LEU C 892 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 894 " --> pdb=" O ILE C 797 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER C 855 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LEU C 893 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 857 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N THR C 895 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL C 859 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 593 through 596 removed outlier: 8.116A pdb=" N PHE D 594 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE D 596 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR D 466 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 570 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N PHE D 465 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY D 572 " --> pdb=" O PHE D 465 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N GLY D 467 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 573 " --> pdb=" O PHE D 530 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 794 through 798 removed outlier: 8.237A pdb=" N ILE D 795 " --> pdb=" O VAL D 890 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU D 892 " --> pdb=" O ILE D 795 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE D 797 " --> pdb=" O LEU D 892 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA D 894 " --> pdb=" O ILE D 797 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER D 855 " --> pdb=" O LEU D 891 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEU D 893 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 857 " --> pdb=" O LEU D 893 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR D 895 " --> pdb=" O VAL D 857 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL D 859 " --> pdb=" O THR D 895 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR D 821 " --> pdb=" O ILE D 856 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR D 858 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR D 823 " --> pdb=" O TYR D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 593 through 595 removed outlier: 8.824A pdb=" N PHE E 594 " --> pdb=" O GLY E 462 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU E 464 " --> pdb=" O PHE E 594 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS E 463 " --> pdb=" O ILE E 568 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL E 570 " --> pdb=" O CYS E 463 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE E 465 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY E 572 " --> pdb=" O PHE E 465 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER E 526 " --> pdb=" O VAL E 569 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ILE E 571 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE E 528 " --> pdb=" O ILE E 571 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA E 492 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE E 529 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE E 494 " --> pdb=" O PHE E 529 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 918 through 920 removed outlier: 8.278A pdb=" N PHE E 919 " --> pdb=" O ARG E 794 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU E 796 " --> pdb=" O PHE E 919 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE E 795 " --> pdb=" O VAL E 890 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU E 892 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE E 797 " --> pdb=" O LEU E 892 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA E 894 " --> pdb=" O ILE E 797 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER E 855 " --> pdb=" O LEU E 891 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU E 893 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL E 857 " --> pdb=" O LEU E 893 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N THR E 895 " --> pdb=" O VAL E 857 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL E 859 " --> pdb=" O THR E 895 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR E 821 " --> pdb=" O ILE E 856 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N TYR E 858 " --> pdb=" O THR E 821 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR E 823 " --> pdb=" O TYR E 858 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 462 through 466 removed outlier: 6.653A pdb=" N VAL F 570 " --> pdb=" O CYS F 463 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE F 465 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY F 572 " --> pdb=" O PHE F 465 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 796 through 798 Processing sheet with id= O, first strand: chain 'F' and resid 855 through 859 710 hydrogen bonds defined for protein. 2079 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: 7.29 Time building geometry restraints manager: 12.03 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: 7828 1.34 - 1.46: 3872 1.46 - 1.58: 13223 1.58 - 1.70: 19 1.70 - 1.81: 155 Bond restraints: 25097 Sorted by residual: bond pdb=" CA ASP D 614 " pdb=" CB ASP D 614 " ideal model delta sigma weight residual 1.527 1.472 0.055 2.48e-02 1.63e+03 5.00e+00 bond pdb=" CG GLU B 626 " pdb=" CD GLU B 626 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CA ARG C 585 " pdb=" CB ARG C 585 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.27e-02 6.20e+03 3.33e+00 bond pdb=" C LYS D 605 " pdb=" N GLU D 606 " ideal model delta sigma weight residual 1.334 1.308 0.026 1.43e-02 4.89e+03 3.27e+00 bond pdb=" O3B ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 1.592 1.539 0.053 3.00e-02 1.11e+03 3.14e+00 ... (remaining 25092 not shown) Histogram of bond angle deviations from ideal: 98.85 - 106.99: 1023 106.99 - 115.12: 15167 115.12 - 123.26: 16724 123.26 - 131.40: 1066 131.40 - 139.54: 48 Bond angle restraints: 34028 Sorted by residual: angle pdb=" N VAL C 907 " pdb=" CA VAL C 907 " pdb=" C VAL C 907 " ideal model delta sigma weight residual 111.90 107.88 4.02 8.10e-01 1.52e+00 2.47e+01 angle pdb=" N VAL B 864 " pdb=" CA VAL B 864 " pdb=" C VAL B 864 " ideal model delta sigma weight residual 113.42 108.12 5.30 1.17e+00 7.31e-01 2.05e+01 angle pdb=" N THR C1373 " pdb=" CA THR C1373 " pdb=" C THR C1373 " ideal model delta sigma weight residual 113.38 108.18 5.20 1.17e+00 7.31e-01 1.98e+01 angle pdb=" N LEU F 431 " pdb=" CA LEU F 431 " pdb=" C LEU F 431 " ideal model delta sigma weight residual 113.21 108.37 4.84 1.15e+00 7.56e-01 1.77e+01 angle pdb=" N THR E 474 " pdb=" CA THR E 474 " pdb=" C THR E 474 " ideal model delta sigma weight residual 113.18 107.65 5.53 1.33e+00 5.65e-01 1.73e+01 ... (remaining 34023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.40: 14579 26.40 - 52.81: 759 52.81 - 79.21: 92 79.21 - 105.61: 14 105.61 - 132.02: 3 Dihedral angle restraints: 15447 sinusoidal: 6479 harmonic: 8968 Sorted by residual: dihedral pdb=" O2A ADP A1301 " pdb=" O3A ADP A1301 " pdb=" PA ADP A1301 " pdb=" PB ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 72.02 -132.02 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C5' ADP A1301 " pdb=" O5' ADP A1301 " pdb=" PA ADP A1301 " pdb=" O2A ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 61.87 -121.87 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP A1301 " pdb=" O3A ADP A1301 " pdb=" PB ADP A1301 " pdb=" PA ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 -176.58 116.58 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 15444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2875 0.051 - 0.103: 801 0.103 - 0.154: 145 0.154 - 0.206: 11 0.206 - 0.257: 4 Chirality restraints: 3836 Sorted by residual: chirality pdb=" CA GLU B 625 " pdb=" N GLU B 625 " pdb=" C GLU B 625 " pdb=" CB GLU B 625 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU F 910 " pdb=" CB LEU F 910 " pdb=" CD1 LEU F 910 " pdb=" CD2 LEU F 910 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE A 912 " pdb=" CA ILE A 912 " pdb=" CG1 ILE A 912 " pdb=" CG2 ILE A 912 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3833 not shown) Planarity restraints: 4361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 586 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO D 587 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 587 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 587 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 524 " -0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO A 525 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 525 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 525 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 575 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" CG ASN D 575 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN D 575 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN D 575 " 0.018 2.00e-02 2.50e+03 ... (remaining 4358 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 5216 2.77 - 3.48: 35936 3.48 - 4.19: 54475 4.19 - 4.90: 92315 Nonbonded interactions: 187944 Sorted by model distance: nonbonded pdb=" CD1 LEU F 717 " pdb=" N LEU F 817 " model vdw 1.353 3.540 nonbonded pdb=" CD1 LEU F 717 " pdb=" CA LEU F 817 " model vdw 2.052 3.890 nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.100 2.440 nonbonded pdb=" OG SER E 690 " pdb=" OE1 GLN E 691 " model vdw 2.114 2.440 nonbonded pdb=" OE2 GLU E 440 " pdb=" OH TYR F 659 " model vdw 2.126 2.440 ... (remaining 187939 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 923)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923)) } ncs_group { reference = (chain 'B' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 945 or resid 1330 through 1389)) selection = (chain 'C' and (resid 422 through 693 or resid 697 through 1389)) selection = (chain 'D' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 1389)) selection = (chain 'E' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 1389)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 7.110 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 66.600 Find NCS groups from input model: 2.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25097 Z= 0.341 Angle : 0.863 12.456 34028 Z= 0.477 Chirality : 0.048 0.257 3836 Planarity : 0.006 0.103 4361 Dihedral : 15.362 132.018 9597 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.71 % Favored : 91.16 % Rotamer: Outliers : 0.15 % Allowed : 0.71 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.58 (0.15), residues: 3019 helix: -0.52 (0.14), residues: 1320 sheet: -0.54 (0.28), residues: 330 loop : -1.66 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 865 HIS 0.009 0.002 HIS A 815 PHE 0.049 0.002 PHE F 877 TYR 0.018 0.002 TYR C 634 ARG 0.013 0.001 ARG F 913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 542 time to evaluate : 3.083 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.2705 (tpp) cc_final: 0.0864 (mmt) REVERT: D 426 ASP cc_start: 0.8506 (p0) cc_final: 0.8237 (p0) REVERT: D 523 MET cc_start: 0.7300 (mpp) cc_final: 0.6979 (mtt) REVERT: D 530 PHE cc_start: 0.8345 (m-80) cc_final: 0.7980 (m-80) REVERT: D 559 MET cc_start: 0.7050 (ttm) cc_final: 0.6826 (mtp) REVERT: E 438 LEU cc_start: 0.8453 (pp) cc_final: 0.8250 (tt) REVERT: E 495 MET cc_start: 0.7396 (ppp) cc_final: 0.6865 (ppp) REVERT: F 615 TRP cc_start: 0.3799 (m-10) cc_final: 0.3314 (m-10) REVERT: F 721 GLN cc_start: 0.5393 (mp10) cc_final: 0.4722 (tp-100) REVERT: F 913 ARG cc_start: 0.0042 (tpt170) cc_final: -0.0184 (ptm-80) outliers start: 4 outliers final: 1 residues processed: 545 average time/residue: 0.4182 time to fit residues: 335.0609 Evaluate side-chains 259 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 237 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN B 808 HIS C 512 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN D 808 HIS ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1330 HIS E 815 HIS F 922 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25097 Z= 0.285 Angle : 0.729 10.449 34028 Z= 0.366 Chirality : 0.046 0.269 3836 Planarity : 0.005 0.086 4361 Dihedral : 10.071 112.583 3486 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.39 % Favored : 92.48 % Rotamer: Outliers : 0.33 % Allowed : 5.79 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.54 (0.15), residues: 3019 helix: -0.56 (0.14), residues: 1319 sheet: -0.51 (0.29), residues: 328 loop : -1.55 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 505 HIS 0.007 0.001 HIS F 861 PHE 0.036 0.002 PHE F 877 TYR 0.028 0.002 TYR A 915 ARG 0.008 0.001 ARG F 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 348 time to evaluate : 2.599 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.5245 (OUTLIER) cc_final: 0.3746 (mmt) REVERT: A 523 MET cc_start: 0.3964 (tpp) cc_final: 0.1891 (mmt) REVERT: A 575 ASN cc_start: 0.0381 (OUTLIER) cc_final: 0.0111 (p0) REVERT: A 611 HIS cc_start: 0.1831 (t-90) cc_final: 0.1597 (t70) REVERT: A 686 MET cc_start: -0.1700 (mtp) cc_final: -0.2871 (tpp) REVERT: B 683 MET cc_start: 0.5754 (tpp) cc_final: 0.5545 (tpp) REVERT: C 1379 MET cc_start: 0.7896 (tpp) cc_final: 0.7640 (mmm) REVERT: D 559 MET cc_start: 0.6983 (ttm) cc_final: 0.6764 (mtp) REVERT: E 438 LEU cc_start: 0.8449 (pp) cc_final: 0.8125 (tt) REVERT: E 938 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5850 (pp) REVERT: F 559 MET cc_start: 0.6209 (tpt) cc_final: 0.3983 (ptt) REVERT: F 615 TRP cc_start: 0.3831 (m-10) cc_final: 0.3475 (m-10) REVERT: F 627 LEU cc_start: 0.7149 (tt) cc_final: 0.6859 (tt) REVERT: F 721 GLN cc_start: 0.5191 (mp10) cc_final: 0.4533 (tp-100) REVERT: F 913 ARG cc_start: 0.0392 (tpt170) cc_final: -0.0020 (ptm-80) outliers start: 9 outliers final: 2 residues processed: 353 average time/residue: 0.3691 time to fit residues: 200.0576 Evaluate side-chains 233 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 228 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 297 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 221 optimal weight: 0.0870 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN B 861 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN D 544 GLN D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 699 GLN E 815 HIS F1335 ASN F1351 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25097 Z= 0.226 Angle : 0.672 10.389 34028 Z= 0.333 Chirality : 0.045 0.253 3836 Planarity : 0.005 0.083 4361 Dihedral : 9.617 102.772 3486 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.78 % Favored : 92.08 % Rotamer: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.46 (0.15), residues: 3019 helix: -0.51 (0.14), residues: 1333 sheet: -0.43 (0.28), residues: 341 loop : -1.51 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 865 HIS 0.005 0.001 HIS B 808 PHE 0.035 0.001 PHE F 877 TYR 0.026 0.001 TYR A 521 ARG 0.006 0.000 ARG D 851 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 331 time to evaluate : 2.938 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.5500 (mtt) cc_final: 0.4436 (mmt) REVERT: A 458 GLN cc_start: -0.0311 (OUTLIER) cc_final: -0.1294 (tt0) REVERT: A 523 MET cc_start: 0.4781 (tpp) cc_final: 0.2395 (mmt) REVERT: A 611 HIS cc_start: 0.1473 (t-90) cc_final: 0.1179 (t-90) REVERT: A 686 MET cc_start: -0.1239 (mtp) cc_final: -0.2587 (tpp) REVERT: A 789 MET cc_start: 0.1391 (ppp) cc_final: -0.1845 (mmt) REVERT: B 823 TYR cc_start: 0.6723 (m-80) cc_final: 0.6091 (m-80) REVERT: B 874 LYS cc_start: 0.7802 (mptt) cc_final: 0.7085 (tptt) REVERT: C 441 MET cc_start: 0.8057 (mtp) cc_final: 0.7635 (mtp) REVERT: C 686 MET cc_start: 0.7145 (mmt) cc_final: 0.6921 (mmm) REVERT: C 851 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7822 (tmm-80) REVERT: D 426 ASP cc_start: 0.8032 (p0) cc_final: 0.7772 (p0) REVERT: D 544 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6959 (pp30) REVERT: D 545 ASP cc_start: 0.8154 (t0) cc_final: 0.7935 (t70) REVERT: E 438 LEU cc_start: 0.8386 (pp) cc_final: 0.8113 (tt) REVERT: E 508 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6972 (mt-10) REVERT: E 686 MET cc_start: 0.6405 (mmp) cc_final: 0.4563 (mmp) REVERT: F 497 LYS cc_start: 0.7153 (mppt) cc_final: 0.6929 (mmmm) REVERT: F 615 TRP cc_start: 0.4296 (m-10) cc_final: 0.3984 (m-10) REVERT: F 721 GLN cc_start: 0.5080 (mp10) cc_final: 0.4504 (tp40) REVERT: F 913 ARG cc_start: 0.0608 (tpt170) cc_final: 0.0099 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 333 average time/residue: 0.3779 time to fit residues: 194.1011 Evaluate side-chains 236 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 131 optimal weight: 0.0870 chunk 185 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 292 optimal weight: 0.0870 chunk 144 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 908 GLN B 616 ASN ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN E 815 HIS F 908 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25097 Z= 0.194 Angle : 0.648 10.184 34028 Z= 0.319 Chirality : 0.044 0.230 3836 Planarity : 0.005 0.079 4361 Dihedral : 9.248 89.494 3486 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.45 % Favored : 92.45 % Rotamer: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.30 (0.15), residues: 3019 helix: -0.39 (0.14), residues: 1322 sheet: -0.25 (0.29), residues: 327 loop : -1.42 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 505 HIS 0.004 0.001 HIS F 611 PHE 0.029 0.001 PHE F 877 TYR 0.014 0.001 TYR B 448 ARG 0.012 0.000 ARG E 540 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 325 time to evaluate : 2.504 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: symmetry clash REVERT: A 441 MET cc_start: 0.5626 (mtt) cc_final: 0.5412 (mtt) REVERT: A 455 PHE cc_start: 0.1386 (m-80) cc_final: 0.1133 (m-10) REVERT: A 523 MET cc_start: 0.5396 (tpp) cc_final: 0.3084 (mmt) REVERT: A 611 HIS cc_start: 0.0523 (t-90) cc_final: 0.0251 (t-90) REVERT: A 789 MET cc_start: 0.1389 (ppp) cc_final: -0.1838 (mmt) REVERT: B 874 LYS cc_start: 0.7890 (mptt) cc_final: 0.7667 (mmtt) REVERT: C 686 MET cc_start: 0.7139 (mmt) cc_final: 0.6925 (mmm) REVERT: C 851 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7879 (tmm-80) REVERT: D 426 ASP cc_start: 0.7952 (p0) cc_final: 0.7717 (p0) REVERT: E 438 LEU cc_start: 0.8366 (pp) cc_final: 0.8105 (tt) REVERT: E 495 MET cc_start: 0.7566 (ppp) cc_final: 0.7320 (ppp) REVERT: E 680 GLU cc_start: 0.7320 (mp0) cc_final: 0.6840 (mp0) REVERT: E 1380 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7807 (pp20) REVERT: F 615 TRP cc_start: 0.4390 (m-10) cc_final: 0.4121 (m-10) REVERT: F 721 GLN cc_start: 0.5605 (mp10) cc_final: 0.4776 (tp40) REVERT: F 808 HIS cc_start: 0.0903 (m170) cc_final: -0.0331 (m-70) REVERT: F 913 ARG cc_start: 0.0723 (tpt170) cc_final: 0.0230 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 327 average time/residue: 0.3626 time to fit residues: 184.7136 Evaluate side-chains 245 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 202 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN E 815 HIS E1346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25097 Z= 0.185 Angle : 0.647 10.446 34028 Z= 0.318 Chirality : 0.044 0.214 3836 Planarity : 0.004 0.063 4361 Dihedral : 8.908 84.931 3486 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.68 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 3019 helix: -0.32 (0.14), residues: 1336 sheet: -0.20 (0.29), residues: 325 loop : -1.39 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 505 HIS 0.005 0.001 HIS D 815 PHE 0.037 0.001 PHE F 877 TYR 0.018 0.001 TYR B 823 ARG 0.006 0.000 ARG B1332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.706 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: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.5312 (tpp) cc_final: 0.3317 (mmt) REVERT: A 611 HIS cc_start: 0.0561 (t-90) cc_final: 0.0289 (t-90) REVERT: A 789 MET cc_start: 0.1251 (ppp) cc_final: -0.1447 (mmt) REVERT: C 686 MET cc_start: 0.7118 (mmt) cc_final: 0.6800 (mmm) REVERT: C 851 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7850 (tmm-80) REVERT: D 426 ASP cc_start: 0.8084 (p0) cc_final: 0.7832 (p0) REVERT: E 820 PHE cc_start: 0.6237 (m-80) cc_final: 0.5626 (m-80) REVERT: F 495 MET cc_start: 0.4632 (mtt) cc_final: 0.4392 (mtp) REVERT: F 615 TRP cc_start: 0.4544 (m-10) cc_final: 0.4310 (m-10) REVERT: F 721 GLN cc_start: 0.5296 (mp10) cc_final: 0.4438 (tp40) REVERT: F 808 HIS cc_start: 0.0943 (m170) cc_final: -0.0377 (m-70) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.3602 time to fit residues: 174.4873 Evaluate side-chains 237 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 chunk 171 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 135 optimal weight: 0.0000 chunk 24 optimal weight: 0.0050 chunk 96 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN B 808 HIS B 844 GLN ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1366 HIS D 691 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25097 Z= 0.163 Angle : 0.641 9.856 34028 Z= 0.313 Chirality : 0.043 0.221 3836 Planarity : 0.004 0.072 4361 Dihedral : 8.569 86.430 3486 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.25 % Favored : 92.61 % Rotamer: Outliers : 0.07 % Allowed : 2.67 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.10 (0.16), residues: 3019 helix: -0.22 (0.14), residues: 1332 sheet: -0.06 (0.29), residues: 331 loop : -1.36 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 505 HIS 0.005 0.001 HIS B 861 PHE 0.040 0.001 PHE B 933 TYR 0.020 0.001 TYR A 823 ARG 0.008 0.000 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 316 time to evaluate : 2.561 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: symmetry clash REVERT: A 441 MET cc_start: 0.6008 (mtm) cc_final: 0.5733 (mmt) REVERT: A 523 MET cc_start: 0.5315 (tpp) cc_final: 0.3388 (mmt) REVERT: A 789 MET cc_start: 0.1126 (ppp) cc_final: -0.1920 (mmt) REVERT: B 683 MET cc_start: 0.5980 (tpp) cc_final: 0.5486 (tpp) REVERT: C 686 MET cc_start: 0.7099 (mmt) cc_final: 0.6861 (mmm) REVERT: C 851 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7830 (tmm-80) REVERT: D 426 ASP cc_start: 0.8033 (p0) cc_final: 0.7763 (p0) REVERT: E 680 GLU cc_start: 0.7221 (mp0) cc_final: 0.6809 (mp0) REVERT: F 615 TRP cc_start: 0.4511 (m-10) cc_final: 0.4297 (m-10) REVERT: F 721 GLN cc_start: 0.4825 (mp10) cc_final: 0.4348 (tp40) REVERT: F 808 HIS cc_start: 0.0656 (m170) cc_final: -0.0520 (m-70) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.3545 time to fit residues: 177.8175 Evaluate side-chains 235 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 246 optimal weight: 0.0370 chunk 163 optimal weight: 1.9990 chunk 292 optimal weight: 0.2980 chunk 182 optimal weight: 5.9990 chunk 178 optimal weight: 0.0020 chunk 134 optimal weight: 0.9980 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN B 808 HIS ** B1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25097 Z= 0.164 Angle : 0.641 11.813 34028 Z= 0.313 Chirality : 0.044 0.309 3836 Planarity : 0.004 0.067 4361 Dihedral : 8.283 87.563 3486 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.45 % Favored : 92.45 % Rotamer: Outliers : 0.04 % Allowed : 1.67 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.01 (0.16), residues: 3019 helix: -0.16 (0.14), residues: 1340 sheet: 0.06 (0.29), residues: 336 loop : -1.33 (0.18), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 865 HIS 0.006 0.001 HIS B 861 PHE 0.040 0.001 PHE F 877 TYR 0.020 0.001 TYR A 823 ARG 0.004 0.000 ARG E 478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 2.876 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.6142 (mtm) cc_final: 0.5774 (mmt) REVERT: A 523 MET cc_start: 0.5445 (tpp) cc_final: 0.3480 (mmt) REVERT: A 789 MET cc_start: 0.1005 (ppp) cc_final: -0.1674 (mmt) REVERT: C 595 LEU cc_start: 0.8486 (tp) cc_final: 0.8257 (tt) REVERT: D 426 ASP cc_start: 0.8069 (p0) cc_final: 0.7792 (p0) REVERT: E 680 GLU cc_start: 0.7301 (mp0) cc_final: 0.7055 (mp0) REVERT: E 820 PHE cc_start: 0.6315 (m-80) cc_final: 0.5946 (m-80) REVERT: F 615 TRP cc_start: 0.4581 (m-10) cc_final: 0.4369 (m-10) REVERT: F 627 LEU cc_start: 0.7215 (tt) cc_final: 0.6977 (tt) REVERT: F 721 GLN cc_start: 0.4823 (mp10) cc_final: 0.4414 (tp40) REVERT: F 808 HIS cc_start: 0.0685 (m170) cc_final: -0.0452 (m-70) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.3512 time to fit residues: 173.0732 Evaluate side-chains 231 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 174 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN B 808 HIS ** B1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** F 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 908 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25097 Z= 0.190 Angle : 0.663 11.814 34028 Z= 0.322 Chirality : 0.044 0.261 3836 Planarity : 0.005 0.063 4361 Dihedral : 8.305 86.717 3486 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.92 % Favored : 91.98 % Rotamer: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -0.99 (0.16), residues: 3019 helix: -0.13 (0.14), residues: 1337 sheet: -0.00 (0.29), residues: 331 loop : -1.29 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 865 HIS 0.006 0.001 HIS B 861 PHE 0.038 0.001 PHE F 877 TYR 0.014 0.001 TYR A 823 ARG 0.010 0.000 ARG B 792 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 2.904 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: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.6368 (mtm) cc_final: 0.5317 (mmt) REVERT: A 523 MET cc_start: 0.5303 (tpp) cc_final: 0.3656 (mmt) REVERT: A 686 MET cc_start: -0.0167 (tmm) cc_final: -0.0391 (ttm) REVERT: A 789 MET cc_start: 0.1054 (ppp) cc_final: -0.1959 (mmt) REVERT: B 683 MET cc_start: 0.5868 (tpp) cc_final: 0.5352 (tpp) REVERT: C 501 CYS cc_start: 0.6596 (p) cc_final: 0.6389 (p) REVERT: C 555 LEU cc_start: 0.8979 (tp) cc_final: 0.8660 (tt) REVERT: D 426 ASP cc_start: 0.8109 (p0) cc_final: 0.7831 (p0) REVERT: D 544 GLN cc_start: 0.7747 (pp30) cc_final: 0.7527 (pp30) REVERT: E 540 ARG cc_start: 0.7801 (tmm160) cc_final: 0.7162 (mmm160) REVERT: E 680 GLU cc_start: 0.7729 (mp0) cc_final: 0.7225 (mp0) REVERT: E 820 PHE cc_start: 0.6330 (m-80) cc_final: 0.6125 (m-80) REVERT: F 615 TRP cc_start: 0.4595 (m-10) cc_final: 0.4292 (m-10) REVERT: F 627 LEU cc_start: 0.7246 (tt) cc_final: 0.6996 (tt) REVERT: F 721 GLN cc_start: 0.4981 (mp10) cc_final: 0.4459 (tp-100) REVERT: F 808 HIS cc_start: 0.0725 (m170) cc_final: -0.0404 (m-70) REVERT: F 927 GLU cc_start: 0.5880 (pm20) cc_final: 0.5625 (mp0) outliers start: 1 outliers final: 1 residues processed: 289 average time/residue: 0.3414 time to fit residues: 156.8606 Evaluate side-chains 225 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 0.4980 chunk 279 optimal weight: 0.7980 chunk 255 optimal weight: 9.9990 chunk 272 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS ** B1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1366 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25097 Z= 0.186 Angle : 0.659 11.689 34028 Z= 0.320 Chirality : 0.043 0.246 3836 Planarity : 0.004 0.063 4361 Dihedral : 8.189 86.179 3486 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.75 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.03 (0.16), residues: 3019 helix: -0.17 (0.14), residues: 1347 sheet: -0.01 (0.29), residues: 334 loop : -1.33 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 865 HIS 0.007 0.001 HIS B 861 PHE 0.037 0.001 PHE F 877 TYR 0.029 0.001 TYR B1356 ARG 0.008 0.000 ARG E 722 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.556 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: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.6390 (mtm) cc_final: 0.5720 (mmt) REVERT: A 523 MET cc_start: 0.5460 (tpp) cc_final: 0.3878 (mmt) REVERT: A 686 MET cc_start: 0.0004 (tmm) cc_final: -0.0254 (ttm) REVERT: A 789 MET cc_start: 0.0990 (ppp) cc_final: -0.0097 (mmt) REVERT: C 686 MET cc_start: 0.7265 (mmt) cc_final: 0.6375 (ppp) REVERT: D 426 ASP cc_start: 0.8058 (p0) cc_final: 0.7833 (p0) REVERT: D 495 MET cc_start: 0.8366 (tmm) cc_final: 0.8072 (tmm) REVERT: E 540 ARG cc_start: 0.7848 (tmm160) cc_final: 0.7204 (mmm160) REVERT: F 442 VAL cc_start: 0.6952 (t) cc_final: 0.6737 (t) REVERT: F 495 MET cc_start: 0.5294 (mtt) cc_final: 0.5066 (mtt) REVERT: F 615 TRP cc_start: 0.4680 (m-10) cc_final: 0.4380 (m-10) REVERT: F 627 LEU cc_start: 0.7268 (tt) cc_final: 0.6996 (tt) REVERT: F 721 GLN cc_start: 0.4769 (mp10) cc_final: 0.4143 (tp-100) REVERT: F 808 HIS cc_start: 0.0748 (m170) cc_final: -0.0360 (m-70) REVERT: F 927 GLU cc_start: 0.5877 (pm20) cc_final: 0.5512 (mp0) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3514 time to fit residues: 157.8743 Evaluate side-chains 219 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 0.0070 chunk 287 optimal weight: 5.9990 chunk 175 optimal weight: 0.0040 chunk 136 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 185 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 overall best weight: 0.8212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS ** B1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1366 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 25097 Z= 0.177 Angle : 0.664 11.555 34028 Z= 0.321 Chirality : 0.044 0.246 3836 Planarity : 0.004 0.062 4361 Dihedral : 7.972 86.755 3486 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.39 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -0.99 (0.16), residues: 3019 helix: -0.17 (0.14), residues: 1346 sheet: 0.07 (0.29), residues: 336 loop : -1.29 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 865 HIS 0.015 0.001 HIS F 900 PHE 0.035 0.001 PHE F 877 TYR 0.017 0.001 TYR A 448 ARG 0.008 0.000 ARG F 913 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 3.090 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 441 MET cc_start: 0.6123 (mtm) cc_final: 0.5888 (mmt) REVERT: A 523 MET cc_start: 0.5399 (tpp) cc_final: 0.3843 (mmt) REVERT: A 686 MET cc_start: -0.0095 (tmm) cc_final: -0.0416 (ttm) REVERT: A 789 MET cc_start: -0.0276 (ppp) cc_final: -0.1578 (mmt) REVERT: C 686 MET cc_start: 0.7251 (mmt) cc_final: 0.6408 (ppp) REVERT: C 844 GLN cc_start: 0.6502 (tp-100) cc_final: 0.6048 (tp-100) REVERT: D 426 ASP cc_start: 0.8020 (p0) cc_final: 0.7804 (p0) REVERT: D 495 MET cc_start: 0.8326 (tmm) cc_final: 0.8030 (tmm) REVERT: D 1379 MET cc_start: 0.8811 (mmm) cc_final: 0.8558 (mmm) REVERT: F 495 MET cc_start: 0.5305 (mtt) cc_final: 0.4971 (mtm) REVERT: F 615 TRP cc_start: 0.4777 (m-10) cc_final: 0.4477 (m-10) REVERT: F 627 LEU cc_start: 0.7254 (tt) cc_final: 0.6983 (tt) REVERT: F 721 GLN cc_start: 0.4597 (mp10) cc_final: 0.3978 (tp-100) REVERT: F 808 HIS cc_start: 0.0844 (m170) cc_final: -0.0204 (m-70) REVERT: F 852 THR cc_start: 0.6331 (m) cc_final: 0.6081 (m) REVERT: F 927 GLU cc_start: 0.5688 (pm20) cc_final: 0.5393 (mp0) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3623 time to fit residues: 164.5261 Evaluate side-chains 215 residues out of total 2695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 5.9990 chunk 256 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 66 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 247 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS ** B1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.143650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.110755 restraints weight = 99918.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.107415 restraints weight = 86015.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.107832 restraints weight = 80421.977| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25097 Z= 0.167 Angle : 0.661 11.432 34028 Z= 0.318 Chirality : 0.043 0.245 3836 Planarity : 0.004 0.062 4361 Dihedral : 7.761 87.574 3486 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.35 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -0.88 (0.16), residues: 3019 helix: -0.11 (0.14), residues: 1336 sheet: 0.23 (0.29), residues: 331 loop : -1.21 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 865 HIS 0.010 0.001 HIS F 900 PHE 0.037 0.001 PHE F 877 TYR 0.014 0.001 TYR B 823 ARG 0.005 0.000 ARG C 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4676.56 seconds wall clock time: 85 minutes 44.03 seconds (5144.03 seconds total)