Starting phenix.real_space_refine on Fri Mar 22 10:15:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ofo_3776/03_2024/5ofo_3776_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ofo_3776/03_2024/5ofo_3776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ofo_3776/03_2024/5ofo_3776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ofo_3776/03_2024/5ofo_3776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ofo_3776/03_2024/5ofo_3776_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ofo_3776/03_2024/5ofo_3776_updated.pdb" } resolution = 4.6 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= 0.001 sd= 0.007 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 33 5.49 5 S 125 5.16 5 C 20516 2.51 5 N 5965 2.21 5 O 6354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "D PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 815": "NH1" <-> "NH2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32993 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 1 Chain: "F" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 661} Chain breaks: 1 Chain: "E" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 660} Chain breaks: 1 Chain: "D" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 661} Chain breaks: 1 Chain: "B" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 660} Chain breaks: 1 Chain: "A" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5442 Classifications: {'peptide': 686} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 1 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.70, per 1000 atoms: 0.51 Number of scatterers: 32993 At special positions: 0 Unit cell: (158.92, 165.77, 180.84, 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 125 16.00 P 33 15.00 O 6354 8.00 N 5965 7.00 C 20516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.77 Conformation dependent library (CDL) restraints added in 5.0 seconds 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 27 sheets defined 56.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.94 Creating SS restraints... Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 254 through 269 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 297 through 304 Proline residue: C 301 - end of helix Processing helix chain 'C' and resid 316 through 323 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 343 through 361 removed outlier: 5.192A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 410 through 429 Processing helix chain 'C' and resid 435 through 438 No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 442 through 492 Processing helix chain 'C' and resid 495 through 502 Processing helix chain 'C' and resid 505 through 522 Processing helix chain 'C' and resid 533 through 544 Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 562 through 569 removed outlier: 3.944A pdb=" N ARG C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 589 Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 640 through 647 removed outlier: 3.667A pdb=" N VAL C 643 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 647 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 661 through 668 Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 684 through 695 Processing helix chain 'C' and resid 722 through 728 removed outlier: 4.935A pdb=" N ARG C 727 " --> pdb=" O ARG C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 748 removed outlier: 4.488A pdb=" N GLU C 744 " --> pdb=" O ASP C 740 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 745 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 756 Processing helix chain 'C' and resid 768 through 788 removed outlier: 3.967A pdb=" N ARG C 781 " --> pdb=" O ILE C 777 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 782 " --> pdb=" O GLN C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 807 Processing helix chain 'C' and resid 813 through 835 Proline residue: C 816 - end of helix removed outlier: 3.746A pdb=" N GLN C 823 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 824 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 825 " --> pdb=" O GLN C 822 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLU C 826 " --> pdb=" O GLN C 823 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN C 827 " --> pdb=" O GLN C 824 " (cutoff:3.500A) Proline residue: C 828 - end of helix removed outlier: 3.611A pdb=" N GLN C 832 " --> pdb=" O LEU C 829 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 834 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 224 Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 242 through 245 No H-bonds generated for 'chain 'F' and resid 242 through 245' Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 297 through 305 Proline residue: F 301 - end of helix Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 327 through 332 removed outlier: 3.503A pdb=" N ARG F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 361 removed outlier: 4.942A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 388 through 406 Processing helix chain 'F' and resid 410 through 430 Processing helix chain 'F' and resid 438 through 440 No H-bonds generated for 'chain 'F' and resid 438 through 440' Processing helix chain 'F' and resid 442 through 492 Processing helix chain 'F' and resid 495 through 502 Processing helix chain 'F' and resid 505 through 523 Processing helix chain 'F' and resid 533 through 543 Processing helix chain 'F' and resid 548 through 552 Processing helix chain 'F' and resid 555 through 569 removed outlier: 5.212A pdb=" N GLU F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN F 564 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 589 Processing helix chain 'F' and resid 611 through 622 Processing helix chain 'F' and resid 641 through 646 Processing helix chain 'F' and resid 661 through 668 Processing helix chain 'F' and resid 679 through 681 No H-bonds generated for 'chain 'F' and resid 679 through 681' Processing helix chain 'F' and resid 684 through 694 Processing helix chain 'F' and resid 719 through 727 removed outlier: 5.892A pdb=" N ARG F 723 " --> pdb=" O LEU F 720 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU F 724 " --> pdb=" O GLY F 721 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG F 727 " --> pdb=" O GLU F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 748 Processing helix chain 'F' and resid 751 through 756 Processing helix chain 'F' and resid 768 through 787 removed outlier: 4.489A pdb=" N ARG F 781 " --> pdb=" O ILE F 777 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU F 782 " --> pdb=" O GLN F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 806 Processing helix chain 'F' and resid 815 through 833 removed outlier: 4.628A pdb=" N ARG F 819 " --> pdb=" O ARG F 815 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN F 827 " --> pdb=" O GLN F 823 " (cutoff:3.500A) Proline residue: F 828 - end of helix Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 212 through 224 Processing helix chain 'E' and resid 254 through 267 Processing helix chain 'E' and resid 299 through 305 Processing helix chain 'E' and resid 316 through 323 Processing helix chain 'E' and resid 327 through 330 No H-bonds generated for 'chain 'E' and resid 327 through 330' Processing helix chain 'E' and resid 343 through 361 removed outlier: 5.386A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 410 through 430 removed outlier: 3.906A pdb=" N ARG E 418 " --> pdb=" O ARG E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 492 removed outlier: 4.431A pdb=" N MET E 443 " --> pdb=" O ARG E 440 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN E 454 " --> pdb=" O LYS E 451 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR E 455 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 463 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS E 466 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU E 478 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU E 479 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 485 " --> pdb=" O ALA E 482 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN E 488 " --> pdb=" O ALA E 485 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL E 492 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 502 Processing helix chain 'E' and resid 505 through 523 Processing helix chain 'E' and resid 534 through 543 Processing helix chain 'E' and resid 549 through 552 No H-bonds generated for 'chain 'E' and resid 549 through 552' Processing helix chain 'E' and resid 555 through 569 removed outlier: 5.239A pdb=" N GLU E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLN E 564 " --> pdb=" O LEU E 560 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG E 569 " --> pdb=" O GLU E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 611 through 622 Processing helix chain 'E' and resid 640 through 646 removed outlier: 3.804A pdb=" N VAL E 643 " --> pdb=" O LYS E 640 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 646 " --> pdb=" O VAL E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 658 Processing helix chain 'E' and resid 661 through 668 Processing helix chain 'E' and resid 679 through 681 No H-bonds generated for 'chain 'E' and resid 679 through 681' Processing helix chain 'E' and resid 684 through 696 Processing helix chain 'E' and resid 720 through 728 removed outlier: 3.938A pdb=" N ARG E 723 " --> pdb=" O LEU E 720 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU E 724 " --> pdb=" O GLY E 721 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU E 726 " --> pdb=" O ARG E 723 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG E 727 " --> pdb=" O GLU E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 748 Processing helix chain 'E' and resid 751 through 756 Processing helix chain 'E' and resid 768 through 785 removed outlier: 3.681A pdb=" N ARG E 781 " --> pdb=" O ILE E 777 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 782 " --> pdb=" O GLN E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 789 No H-bonds generated for 'chain 'E' and resid 787 through 789' Processing helix chain 'E' and resid 797 through 806 Processing helix chain 'E' and resid 814 through 824 removed outlier: 3.945A pdb=" N GLN E 823 " --> pdb=" O ALA E 820 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E 824 " --> pdb=" O ILE E 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 826 through 835 Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 212 through 224 Processing helix chain 'D' and resid 242 through 245 No H-bonds generated for 'chain 'D' and resid 242 through 245' Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 316 through 321 Processing helix chain 'D' and resid 327 through 330 No H-bonds generated for 'chain 'D' and resid 327 through 330' Processing helix chain 'D' and resid 343 through 361 removed outlier: 5.077A pdb=" N GLU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 435 through 492 removed outlier: 4.758A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N MET D 443 " --> pdb=" O LYS D 439 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 502 Processing helix chain 'D' and resid 505 through 523 Processing helix chain 'D' and resid 533 through 543 Processing helix chain 'D' and resid 550 through 560 removed outlier: 4.260A pdb=" N SER D 554 " --> pdb=" O MET D 551 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 555 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG D 556 " --> pdb=" O GLU D 553 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 557 " --> pdb=" O SER D 554 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 559 " --> pdb=" O ARG D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 569 removed outlier: 3.867A pdb=" N ARG D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 589 Processing helix chain 'D' and resid 611 through 622 Processing helix chain 'D' and resid 641 through 646 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 661 through 668 Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 684 through 694 Processing helix chain 'D' and resid 734 through 748 removed outlier: 4.220A pdb=" N GLU D 744 " --> pdb=" O ASP D 740 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE D 748 " --> pdb=" O GLU D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 755 Processing helix chain 'D' and resid 768 through 789 removed outlier: 3.960A pdb=" N LYS D 780 " --> pdb=" O GLN D 776 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG D 781 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 782 " --> pdb=" O GLN D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 807 Processing helix chain 'D' and resid 817 through 834 removed outlier: 4.657A pdb=" N ASN D 827 " --> pdb=" O GLN D 823 " (cutoff:3.500A) Proline residue: D 828 - end of helix Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 243 through 248 removed outlier: 5.336A pdb=" N GLY B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 4.114A pdb=" N GLY B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.024A pdb=" N ARG B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 361 removed outlier: 5.202A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 410 through 429 removed outlier: 3.954A pdb=" N ALA B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 438 No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 442 through 492 removed outlier: 3.744A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 502 Processing helix chain 'B' and resid 505 through 523 Processing helix chain 'B' and resid 533 through 543 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 562 through 569 removed outlier: 3.612A pdb=" N ARG B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 588 Processing helix chain 'B' and resid 611 through 622 Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.785A pdb=" N VAL B 643 " --> pdb=" O LYS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 668 removed outlier: 3.923A pdb=" N ALA B 665 " --> pdb=" O TYR B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 684 through 694 Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 734 through 747 Processing helix chain 'B' and resid 751 through 755 Processing helix chain 'B' and resid 768 through 787 removed outlier: 3.962A pdb=" N ARG B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 805 Processing helix chain 'B' and resid 813 through 834 Proline residue: B 816 - end of helix removed outlier: 3.687A pdb=" N GLN B 823 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 824 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 825 " --> pdb=" O GLN B 822 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B 826 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN B 827 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Proline residue: B 828 - end of helix removed outlier: 3.824A pdb=" N GLN B 831 " --> pdb=" O PRO B 828 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 833 " --> pdb=" O ALA B 830 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 834 " --> pdb=" O GLN B 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 343 through 361 removed outlier: 5.676A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 410 through 430 removed outlier: 3.912A pdb=" N ARG A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 492 removed outlier: 4.144A pdb=" N ARG A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 441 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A 442 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 443 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 447 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN A 454 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 459 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 469 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 484 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 492 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 506 through 523 Processing helix chain 'A' and resid 533 through 544 Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 555 through 569 removed outlier: 5.324A pdb=" N GLU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.822A pdb=" N VAL A 643 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 646 " --> pdb=" O VAL A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 661 through 668 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.847A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 728 No H-bonds generated for 'chain 'A' and resid 725 through 728' Processing helix chain 'A' and resid 734 through 748 Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 768 through 789 removed outlier: 4.104A pdb=" N ARG A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 782 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 789 " --> pdb=" O ARG A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 806 Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 826 through 834 Processing sheet with id= A, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.560A pdb=" N ILE C 274 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU C 240 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE C 276 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 333 through 337 removed outlier: 7.282A pdb=" N ASN C 201 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL C 336 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 203 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 312 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 204 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 206 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 759 through 762 removed outlier: 3.857A pdb=" N GLU C 759 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 717 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 698 through 700 Processing sheet with id= E, first strand: chain 'C' and resid 793 through 795 removed outlier: 7.076A pdb=" N ILE C 844 " --> pdb=" O HIS C 794 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 165 through 167 removed outlier: 3.744A pdb=" N LEU F 238 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE F 276 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU F 240 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 602 through 605 Processing sheet with id= H, first strand: chain 'F' and resid 629 through 633 removed outlier: 6.643A pdb=" N VAL F 673 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE F 632 " --> pdb=" O VAL F 673 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU F 675 " --> pdb=" O ILE F 632 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 713 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU F 676 " --> pdb=" O VAL F 713 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE F 715 " --> pdb=" O LEU F 676 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'F' and resid 698 through 700 Processing sheet with id= J, first strand: chain 'F' and resid 792 through 795 Processing sheet with id= K, first strand: chain 'E' and resid 333 through 338 removed outlier: 6.610A pdb=" N ASN E 201 " --> pdb=" O GLN E 334 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL E 336 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL E 203 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 338 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 205 " --> pdb=" O VAL E 338 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 236 through 239 Processing sheet with id= M, first strand: chain 'E' and resid 759 through 762 removed outlier: 6.049A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 698 through 700 Processing sheet with id= O, first strand: chain 'E' and resid 792 through 795 removed outlier: 3.672A pdb=" N VAL E 856 " --> pdb=" O ARG E 845 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 334 through 338 removed outlier: 7.017A pdb=" N CYS D 310 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N LEU D 204 " --> pdb=" O CYS D 310 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY D 312 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLY D 206 " --> pdb=" O GLY D 312 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR D 314 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N VAL D 311 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 275 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ALA D 313 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE D 277 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 759 through 762 removed outlier: 3.807A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 714 " --> pdb=" O PHE D 601 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N PHE D 603 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N MET D 716 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 698 through 700 Processing sheet with id= S, first strand: chain 'D' and resid 793 through 795 removed outlier: 6.485A pdb=" N ILE D 844 " --> pdb=" O HIS D 794 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 334 through 337 removed outlier: 3.529A pdb=" N ILE B 205 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS B 310 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N LEU B 204 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY B 312 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL B 311 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 275 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASP B 278 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.968A pdb=" N GLU B 759 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 602 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N PHE B 601 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 714 " --> pdb=" O PHE B 601 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N PHE B 603 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET B 716 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER B 672 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE B 715 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE B 674 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR B 717 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU B 676 " --> pdb=" O THR B 717 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 698 through 700 Processing sheet with id= W, first strand: chain 'B' and resid 845 through 848 Processing sheet with id= X, first strand: chain 'A' and resid 165 through 167 Processing sheet with id= Y, first strand: chain 'A' and resid 333 through 337 removed outlier: 7.069A pdb=" N ASN A 201 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL A 336 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 203 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 759 through 762 removed outlier: 4.031A pdb=" N GLY A 599 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 601 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER A 672 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ILE A 715 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 698 through 700 1571 hydrogen bonds defined for protein. 4329 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: 12.19 Time building geometry restraints manager: 14.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 5968 1.32 - 1.48: 12297 1.48 - 1.63: 14943 1.63 - 1.79: 98 1.79 - 1.95: 129 Bond restraints: 33435 Sorted by residual: bond pdb=" C GLN B 385 " pdb=" N LEU B 386 " ideal model delta sigma weight residual 1.331 1.162 0.169 3.12e-02 1.03e+03 2.92e+01 bond pdb=" O2B AGS D 902 " pdb=" PB AGS D 902 " ideal model delta sigma weight residual 1.531 1.455 0.076 1.60e-02 3.91e+03 2.26e+01 bond pdb=" CA ARG D 183 " pdb=" CB ARG D 183 " ideal model delta sigma weight residual 1.528 1.462 0.065 1.39e-02 5.18e+03 2.19e+01 bond pdb=" C VAL D 760 " pdb=" N VAL D 761 " ideal model delta sigma weight residual 1.329 1.277 0.053 1.17e-02 7.31e+03 2.04e+01 bond pdb=" O2A AGS C 902 " pdb=" PA AGS C 902 " ideal model delta sigma weight residual 1.531 1.461 0.070 1.60e-02 3.91e+03 1.92e+01 ... (remaining 33430 not shown) Histogram of bond angle deviations from ideal: 95.93 - 103.80: 448 103.80 - 111.66: 15427 111.66 - 119.53: 13338 119.53 - 127.39: 15625 127.39 - 135.26: 254 Bond angle restraints: 45092 Sorted by residual: angle pdb=" C VAL B 548 " pdb=" N SER B 549 " pdb=" CA SER B 549 " ideal model delta sigma weight residual 121.70 134.52 -12.82 1.80e+00 3.09e-01 5.07e+01 angle pdb=" C LYS C 747 " pdb=" N ILE C 748 " pdb=" CA ILE C 748 " ideal model delta sigma weight residual 122.77 115.71 7.06 1.05e+00 9.07e-01 4.52e+01 angle pdb=" C VAL C 531 " pdb=" N THR C 532 " pdb=" CA THR C 532 " ideal model delta sigma weight residual 121.70 133.12 -11.42 1.80e+00 3.09e-01 4.03e+01 angle pdb=" C ARG D 440 " pdb=" N LEU D 441 " pdb=" CA LEU D 441 " ideal model delta sigma weight residual 121.54 133.43 -11.89 1.91e+00 2.74e-01 3.88e+01 angle pdb=" C VAL A 246 " pdb=" N ALA A 247 " pdb=" CA ALA A 247 " ideal model delta sigma weight residual 121.70 132.74 -11.04 1.80e+00 3.09e-01 3.76e+01 ... (remaining 45087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 20496 32.04 - 64.08: 346 64.08 - 96.11: 54 96.11 - 128.15: 7 128.15 - 160.19: 5 Dihedral angle restraints: 20908 sinusoidal: 9016 harmonic: 11892 Sorted by residual: dihedral pdb=" CA ASN D 849 " pdb=" C ASN D 849 " pdb=" N GLU D 850 " pdb=" CA GLU D 850 " ideal model delta harmonic sigma weight residual -180.00 -116.47 -63.53 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA TYR A 322 " pdb=" C TYR A 322 " pdb=" N ILE A 323 " pdb=" CA ILE A 323 " ideal model delta harmonic sigma weight residual 180.00 123.76 56.24 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA GLU E 850 " pdb=" C GLU E 850 " pdb=" N ASP E 851 " pdb=" CA ASP E 851 " ideal model delta harmonic sigma weight residual -180.00 -129.93 -50.07 0 5.00e+00 4.00e-02 1.00e+02 ... (remaining 20905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4979 0.144 - 0.288: 110 0.288 - 0.433: 4 0.433 - 0.577: 4 0.577 - 0.721: 3 Chirality restraints: 5100 Sorted by residual: chirality pdb=" PB AGS B 901 " pdb=" O2B AGS B 901 " pdb=" O3A AGS B 901 " pdb=" O3B AGS B 901 " both_signs ideal model delta sigma weight residual True 3.18 2.46 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" PB AGS C 902 " pdb=" O2B AGS C 902 " pdb=" O3A AGS C 902 " pdb=" O3B AGS C 902 " both_signs ideal model delta sigma weight residual True 3.18 2.51 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" PB AGS E 902 " pdb=" O2B AGS E 902 " pdb=" O3A AGS E 902 " pdb=" O3B AGS E 902 " both_signs ideal model delta sigma weight residual True 3.18 2.54 0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 5097 not shown) Planarity restraints: 5885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 850 " -0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C GLU F 850 " 0.103 2.00e-02 2.50e+03 pdb=" O GLU F 850 " -0.038 2.00e-02 2.50e+03 pdb=" N ASP F 851 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 850 " -0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C GLU D 850 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU D 850 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP D 851 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 849 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ASN F 849 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN F 849 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU F 850 " 0.024 2.00e-02 2.50e+03 ... (remaining 5882 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6080 2.76 - 3.29: 33509 3.29 - 3.83: 56807 3.83 - 4.36: 68570 4.36 - 4.90: 107941 Nonbonded interactions: 272907 Sorted by model distance: nonbonded pdb=" OE1 GLU C 658 " pdb=" OH TYR B 656 " model vdw 2.219 2.440 nonbonded pdb=" O SER C 672 " pdb=" OG1 THR C 712 " model vdw 2.221 2.440 nonbonded pdb=" OG SER B 625 " pdb=" OE1 GLU B 627 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR B 612 " pdb=" O2G AGS B 902 " model vdw 2.229 2.440 nonbonded pdb=" O ILE C 745 " pdb=" N PHE C 749 " model vdw 2.233 2.520 ... (remaining 272902 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' selection = (chain 'B' and (resid 161 through 857 or resid 901)) selection = (chain 'C' and (resid 161 through 857 or resid 901)) selection = (chain 'D' and (resid 161 through 857 or resid 901)) selection = (chain 'E' and (resid 161 through 857 or resid 901)) selection = (chain 'F' and (resid 161 through 857 or resid 901)) } 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: 0.960 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: 5.430 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 84.660 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.220 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: 0.000 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 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 : 0.009 0.169 33435 Z= 0.570 Angle : 1.237 12.939 45092 Z= 0.705 Chirality : 0.063 0.721 5100 Planarity : 0.008 0.090 5885 Dihedral : 12.784 160.188 13216 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.40 % Rotamer: Outliers : 0.92 % Allowed : 4.70 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -3.79 (0.11), residues: 4092 helix: -2.84 (0.07), residues: 2390 sheet: -1.14 (0.26), residues: 349 loop : -1.79 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP A 543 HIS 0.022 0.003 HIS F 734 PHE 0.035 0.004 PHE A 255 TYR 0.046 0.004 TYR F 783 ARG 0.030 0.002 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 648 time to evaluate : 3.904 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: 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: 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: 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: 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: C 370 ILE cc_start: 0.8825 (pt) cc_final: 0.8597 (mm) REVERT: C 602 LEU cc_start: 0.7779 (tp) cc_final: 0.7359 (tp) REVERT: F 333 PHE cc_start: 0.5632 (m-80) cc_final: 0.5417 (m-80) REVERT: F 422 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8397 (tt) REVERT: F 686 VAL cc_start: 0.6323 (t) cc_final: 0.5889 (p) REVERT: E 618 LEU cc_start: 0.7476 (tp) cc_final: 0.7204 (tp) REVERT: D 308 LEU cc_start: 0.6944 (pt) cc_final: 0.6674 (mt) REVERT: D 401 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8759 (tt) REVERT: D 602 LEU cc_start: 0.7836 (tp) cc_final: 0.7596 (tp) REVERT: D 641 HIS cc_start: 0.5504 (OUTLIER) cc_final: 0.4411 (m-70) REVERT: D 709 PHE cc_start: 0.7076 (m-10) cc_final: 0.6862 (m-10) REVERT: D 797 ASP cc_start: 0.6087 (p0) cc_final: 0.5711 (p0) REVERT: B 584 ILE cc_start: 0.9249 (mt) cc_final: 0.8889 (tp) REVERT: B 602 LEU cc_start: 0.6402 (tp) cc_final: 0.5923 (tp) REVERT: A 283 MET cc_start: 0.6312 (mmt) cc_final: 0.6081 (mmm) REVERT: A 333 PHE cc_start: 0.6731 (m-80) cc_final: 0.6521 (m-10) REVERT: A 403 MET cc_start: 0.7564 (ttp) cc_final: 0.7255 (ppp) REVERT: A 817 LEU cc_start: 0.6932 (tp) cc_final: 0.6380 (tt) outliers start: 32 outliers final: 5 residues processed: 678 average time/residue: 0.5362 time to fit residues: 541.9849 Evaluate side-chains 319 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 311 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 0.3980 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 HIS C 806 ASN C 824 GLN F 201 ASN ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN F 512 GLN F 595 ASN F 703 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 GLN E 620 ASN E 641 HIS E 755 ASN E 770 HIS E 778 GLN E 822 GLN D 360 HIS D 512 GLN D 595 ASN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN D 719 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 822 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 264 ASN B 297 ASN B 683 HIS B 692 GLN B 703 GLN B 831 GLN B 849 ASN A 174 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A 488 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN A 778 GLN A 806 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33435 Z= 0.222 Angle : 0.734 16.181 45092 Z= 0.382 Chirality : 0.045 0.253 5100 Planarity : 0.006 0.110 5885 Dihedral : 10.755 150.750 4768 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 0.20 % Allowed : 3.29 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.12), residues: 4092 helix: -1.32 (0.09), residues: 2420 sheet: -0.86 (0.25), residues: 368 loop : -1.38 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 543 HIS 0.008 0.001 HIS B 683 PHE 0.022 0.002 PHE A 601 TYR 0.023 0.002 TYR D 503 ARG 0.014 0.001 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 408 time to evaluate : 3.710 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: 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: 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: 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: C 240 LEU cc_start: 0.7214 (tp) cc_final: 0.6932 (tp) REVERT: C 540 LEU cc_start: 0.8698 (tt) cc_final: 0.8420 (tt) REVERT: C 602 LEU cc_start: 0.7825 (tp) cc_final: 0.7576 (tp) REVERT: E 719 ASN cc_start: 0.6452 (t0) cc_final: 0.5752 (t0) REVERT: D 308 LEU cc_start: 0.7252 (pt) cc_final: 0.6842 (mt) REVERT: D 401 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8778 (tt) REVERT: D 602 LEU cc_start: 0.7867 (tp) cc_final: 0.7481 (tp) REVERT: D 618 LEU cc_start: 0.7140 (tt) cc_final: 0.6643 (tt) REVERT: B 602 LEU cc_start: 0.6743 (tp) cc_final: 0.6496 (tp) REVERT: A 584 ILE cc_start: 0.8839 (mt) cc_final: 0.8483 (tp) outliers start: 7 outliers final: 2 residues processed: 414 average time/residue: 0.4849 time to fit residues: 313.3211 Evaluate side-chains 275 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 272 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 308 optimal weight: 2.9990 chunk 252 optimal weight: 0.0870 chunk 102 optimal weight: 5.9990 chunk 371 optimal weight: 0.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 0.0970 chunk 297 optimal weight: 8.9990 overall best weight: 2.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 427 GLN F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 822 GLN E 174 GLN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 GLN E 512 GLN E 620 ASN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 737 ASN B 824 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33435 Z= 0.210 Angle : 0.663 13.292 45092 Z= 0.347 Chirality : 0.044 0.264 5100 Planarity : 0.005 0.068 5885 Dihedral : 10.237 148.601 4768 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 4092 helix: -0.75 (0.10), residues: 2418 sheet: -0.68 (0.26), residues: 360 loop : -1.12 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 543 HIS 0.007 0.001 HIS E 683 PHE 0.020 0.002 PHE A 749 TYR 0.020 0.002 TYR F 503 ARG 0.008 0.001 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 339 time to evaluate : 4.117 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 540 LEU cc_start: 0.8667 (tt) cc_final: 0.8465 (tt) REVERT: C 562 MET cc_start: 0.7945 (mmp) cc_final: 0.7717 (mmp) REVERT: E 602 LEU cc_start: 0.6642 (mm) cc_final: 0.6383 (mm) REVERT: E 719 ASN cc_start: 0.6354 (t0) cc_final: 0.5793 (t0) REVERT: D 401 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8752 (tt) REVERT: D 602 LEU cc_start: 0.7835 (tp) cc_final: 0.7439 (tp) REVERT: D 709 PHE cc_start: 0.6675 (m-10) cc_final: 0.6420 (m-10) REVERT: B 602 LEU cc_start: 0.6905 (tp) cc_final: 0.6636 (tp) REVERT: B 615 CYS cc_start: 0.7364 (p) cc_final: 0.6901 (t) REVERT: A 190 THR cc_start: 0.7933 (p) cc_final: 0.7601 (p) REVERT: A 242 MET cc_start: -0.1379 (ttp) cc_final: -0.1725 (tpt) REVERT: A 329 LEU cc_start: 0.6059 (mp) cc_final: 0.5707 (mp) REVERT: A 638 MET cc_start: 0.6335 (mmp) cc_final: 0.5967 (mmp) outliers start: 2 outliers final: 0 residues processed: 341 average time/residue: 0.4657 time to fit residues: 251.9596 Evaluate side-chains 243 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 4.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.0770 chunk 279 optimal weight: 2.9990 chunk 192 optimal weight: 40.0000 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 chunk 372 optimal weight: 7.9990 chunk 394 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN C 824 GLN ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 849 ASN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 GLN E 512 GLN E 620 ASN E 719 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS B 737 ASN A 360 HIS ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 734 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33435 Z= 0.163 Angle : 0.625 13.839 45092 Z= 0.321 Chirality : 0.043 0.212 5100 Planarity : 0.005 0.057 5885 Dihedral : 9.800 146.798 4768 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.00 (0.13), residues: 4092 helix: -0.37 (0.10), residues: 2427 sheet: -0.46 (0.26), residues: 370 loop : -0.98 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 543 HIS 0.005 0.001 HIS E 683 PHE 0.019 0.001 PHE E 749 TYR 0.018 0.001 TYR B 322 ARG 0.012 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 3.891 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 240 LEU cc_start: 0.7149 (tp) cc_final: 0.6902 (tp) REVERT: C 562 MET cc_start: 0.7833 (mmp) cc_final: 0.7586 (mmp) REVERT: C 602 LEU cc_start: 0.8000 (tp) cc_final: 0.7233 (tp) REVERT: C 777 ILE cc_start: 0.7816 (pt) cc_final: 0.7533 (tp) REVERT: F 551 MET cc_start: 0.5913 (pmm) cc_final: 0.5413 (pmm) REVERT: F 622 MET cc_start: 0.5112 (ptm) cc_final: 0.4692 (ttp) REVERT: E 616 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7579 (ptpp) REVERT: D 401 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8755 (tt) REVERT: D 709 PHE cc_start: 0.6851 (m-10) cc_final: 0.6408 (m-10) REVERT: B 615 CYS cc_start: 0.7187 (p) cc_final: 0.6651 (t) REVERT: A 242 MET cc_start: -0.1617 (ttp) cc_final: -0.2080 (tpt) REVERT: A 646 LEU cc_start: 0.6693 (pt) cc_final: 0.6274 (pp) outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.4561 time to fit residues: 250.8316 Evaluate side-chains 247 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 336 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 0.0570 chunk 99 optimal weight: 5.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 GLN D 512 GLN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 703 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN A 827 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33435 Z= 0.171 Angle : 0.606 9.332 45092 Z= 0.314 Chirality : 0.042 0.257 5100 Planarity : 0.005 0.056 5885 Dihedral : 9.543 143.144 4768 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.07 % Rotamer: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4092 helix: -0.05 (0.10), residues: 2428 sheet: -0.45 (0.26), residues: 377 loop : -0.86 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 543 HIS 0.006 0.001 HIS F 362 PHE 0.017 0.001 PHE E 621 TYR 0.022 0.001 TYR D 503 ARG 0.008 0.000 ARG D 852 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 3.963 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: 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: C 242 MET cc_start: 0.7771 (mmm) cc_final: 0.7550 (mmp) REVERT: C 602 LEU cc_start: 0.8127 (tp) cc_final: 0.7735 (tp) REVERT: F 551 MET cc_start: 0.6070 (pmm) cc_final: 0.5861 (pmm) REVERT: E 298 MET cc_start: 0.6997 (pmm) cc_final: 0.6711 (pmm) REVERT: E 719 ASN cc_start: 0.6994 (t0) cc_final: 0.6524 (t0) REVERT: D 190 THR cc_start: 0.8809 (p) cc_final: 0.8562 (p) REVERT: D 602 LEU cc_start: 0.7882 (tp) cc_final: 0.7356 (tp) REVERT: D 709 PHE cc_start: 0.7002 (m-10) cc_final: 0.6638 (m-10) REVERT: A 242 MET cc_start: -0.1532 (ttp) cc_final: -0.1898 (tpt) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.4819 time to fit residues: 242.5383 Evaluate side-chains 229 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 3.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.6980 chunk 355 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 4.9990 chunk 327 optimal weight: 20.0000 chunk 182 optimal weight: 0.0070 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 ASN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 GLN E 620 ASN E 857 GLN ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN A 512 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33435 Z= 0.232 Angle : 0.634 9.466 45092 Z= 0.329 Chirality : 0.043 0.280 5100 Planarity : 0.005 0.057 5885 Dihedral : 9.449 142.916 4768 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.03 % Allowed : 2.15 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.49 (0.13), residues: 4092 helix: 0.10 (0.10), residues: 2450 sheet: -0.64 (0.25), residues: 380 loop : -0.78 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 543 HIS 0.009 0.001 HIS E 641 PHE 0.019 0.002 PHE B 687 TYR 0.016 0.002 TYR A 319 ARG 0.012 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 3.838 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: 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: symmetry clash revert: symmetry clash REVERT: C 298 MET cc_start: 0.7666 (pmm) cc_final: 0.7392 (pmm) REVERT: E 719 ASN cc_start: 0.7188 (t0) cc_final: 0.6874 (t0) REVERT: D 602 LEU cc_start: 0.7856 (tp) cc_final: 0.7320 (tp) REVERT: D 709 PHE cc_start: 0.7067 (m-10) cc_final: 0.6837 (m-10) REVERT: A 242 MET cc_start: -0.1265 (ttp) cc_final: -0.1533 (tpt) REVERT: A 551 MET cc_start: 0.4977 (mtp) cc_final: 0.4319 (mtm) REVERT: A 646 LEU cc_start: 0.6743 (pt) cc_final: 0.6336 (pp) outliers start: 1 outliers final: 1 residues processed: 293 average time/residue: 0.4357 time to fit residues: 208.1048 Evaluate side-chains 215 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN ** E 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 849 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 488 GLN B 823 GLN A 427 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33435 Z= 0.237 Angle : 0.652 9.863 45092 Z= 0.336 Chirality : 0.043 0.246 5100 Planarity : 0.005 0.066 5885 Dihedral : 9.399 141.181 4768 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.45 (0.13), residues: 4092 helix: 0.13 (0.10), residues: 2455 sheet: -0.64 (0.25), residues: 384 loop : -0.77 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 543 HIS 0.007 0.001 HIS F 362 PHE 0.016 0.002 PHE B 687 TYR 0.016 0.002 TYR F 322 ARG 0.009 0.001 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 3.747 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: 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: symmetry clash REVERT: F 551 MET cc_start: 0.5965 (pmm) cc_final: 0.5234 (pmm) REVERT: E 552 MET cc_start: 0.7209 (ppp) cc_final: 0.6274 (mpp) REVERT: D 602 LEU cc_start: 0.7858 (tp) cc_final: 0.7493 (tp) REVERT: B 562 MET cc_start: 0.7826 (ttp) cc_final: 0.7495 (ttp) REVERT: A 280 LEU cc_start: 0.6752 (pt) cc_final: 0.6454 (pt) REVERT: A 551 MET cc_start: 0.4959 (mtp) cc_final: 0.4491 (mtm) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.4390 time to fit residues: 209.1109 Evaluate side-chains 210 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN D 321 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 703 GLN A 502 GLN A 512 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33435 Z= 0.166 Angle : 0.612 10.196 45092 Z= 0.310 Chirality : 0.043 0.227 5100 Planarity : 0.004 0.063 5885 Dihedral : 9.241 142.348 4768 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4092 helix: 0.32 (0.10), residues: 2445 sheet: -0.47 (0.25), residues: 378 loop : -0.71 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 543 HIS 0.006 0.001 HIS F 362 PHE 0.017 0.002 PHE B 687 TYR 0.014 0.001 TYR A 319 ARG 0.007 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.900 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 552 MET cc_start: 0.5531 (ptp) cc_final: 0.4970 (ptp) REVERT: F 551 MET cc_start: 0.6011 (pmm) cc_final: 0.5354 (pmm) REVERT: D 602 LEU cc_start: 0.7928 (tp) cc_final: 0.7484 (tp) REVERT: D 709 PHE cc_start: 0.6602 (m-10) cc_final: 0.6111 (m-10) REVERT: B 562 MET cc_start: 0.7946 (ttp) cc_final: 0.7411 (ttp) REVERT: A 280 LEU cc_start: 0.6691 (pt) cc_final: 0.6454 (pt) REVERT: A 335 LYS cc_start: 0.7104 (mttt) cc_final: 0.6899 (mttt) REVERT: A 551 MET cc_start: 0.4910 (mtp) cc_final: 0.4494 (mtm) REVERT: A 638 MET cc_start: 0.7209 (mmp) cc_final: 0.6993 (mmp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.4205 time to fit residues: 198.8858 Evaluate side-chains 219 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 5.9990 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 366 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 287 optimal weight: 0.0670 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 0.0570 chunk 365 optimal weight: 6.9990 overall best weight: 3.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 HIS ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN ** E 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 719 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN A 502 GLN A 512 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33435 Z= 0.234 Angle : 0.656 10.983 45092 Z= 0.336 Chirality : 0.043 0.263 5100 Planarity : 0.005 0.104 5885 Dihedral : 9.244 138.564 4768 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.25 (0.13), residues: 4092 helix: 0.28 (0.10), residues: 2450 sheet: -0.48 (0.26), residues: 369 loop : -0.70 (0.19), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 543 HIS 0.011 0.001 HIS C 362 PHE 0.020 0.002 PHE F 753 TYR 0.012 0.002 TYR F 503 ARG 0.011 0.001 ARG E 668 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.961 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 551 MET cc_start: 0.6309 (pmm) cc_final: 0.5639 (pmm) REVERT: D 602 LEU cc_start: 0.7828 (tp) cc_final: 0.7413 (tp) REVERT: D 709 PHE cc_start: 0.6733 (m-10) cc_final: 0.6233 (m-10) REVERT: B 562 MET cc_start: 0.8092 (ttp) cc_final: 0.7782 (ttp) REVERT: A 335 LYS cc_start: 0.7309 (mttt) cc_final: 0.7104 (mttt) REVERT: A 638 MET cc_start: 0.7275 (mmp) cc_final: 0.7054 (mmp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.4122 time to fit residues: 191.6061 Evaluate side-chains 202 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 2.9990 chunk 387 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 406 optimal weight: 8.9990 chunk 374 optimal weight: 7.9990 chunk 323 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN E 719 ASN D 321 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 272 ASN A 502 GLN A 512 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33435 Z= 0.199 Angle : 0.638 12.170 45092 Z= 0.326 Chirality : 0.043 0.269 5100 Planarity : 0.005 0.079 5885 Dihedral : 9.177 140.326 4768 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.18 (0.13), residues: 4092 helix: 0.34 (0.10), residues: 2449 sheet: -0.49 (0.26), residues: 380 loop : -0.67 (0.19), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 543 HIS 0.006 0.001 HIS F 362 PHE 0.018 0.002 PHE F 621 TYR 0.013 0.001 TYR B 812 ARG 0.009 0.000 ARG E 668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 4.292 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 602 LEU cc_start: 0.7912 (tp) cc_final: 0.7299 (tp) REVERT: F 551 MET cc_start: 0.6292 (pmm) cc_final: 0.5654 (pmm) REVERT: D 242 MET cc_start: 0.7275 (tpp) cc_final: 0.6982 (tpp) REVERT: D 602 LEU cc_start: 0.7790 (tp) cc_final: 0.7384 (tp) REVERT: D 709 PHE cc_start: 0.6735 (m-10) cc_final: 0.6152 (m-10) REVERT: B 562 MET cc_start: 0.8017 (ttp) cc_final: 0.7699 (ttp) REVERT: A 638 MET cc_start: 0.7256 (mmp) cc_final: 0.7019 (mmp) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.4408 time to fit residues: 196.5708 Evaluate side-chains 209 residues out of total 3492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.7980 chunk 344 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 0.0270 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 GLN ** F 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN E 719 ASN D 321 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN A 512 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.055237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040297 restraints weight = 278689.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.041476 restraints weight = 179549.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042542 restraints weight = 126858.918| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33435 Z= 0.182 Angle : 0.643 11.512 45092 Z= 0.325 Chirality : 0.043 0.266 5100 Planarity : 0.005 0.075 5885 Dihedral : 9.118 134.999 4768 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.13 (0.13), residues: 4092 helix: 0.37 (0.10), residues: 2459 sheet: -0.45 (0.26), residues: 389 loop : -0.63 (0.19), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 543 HIS 0.006 0.001 HIS F 362 PHE 0.022 0.002 PHE F 621 TYR 0.015 0.001 TYR A 319 ARG 0.006 0.000 ARG E 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5983.31 seconds wall clock time: 109 minutes 49.28 seconds (6589.28 seconds total)