Starting phenix.real_space_refine on Sun Sep 29 19:24:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/09_2024/7ngl_12315_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/09_2024/7ngl_12315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/09_2024/7ngl_12315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/09_2024/7ngl_12315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/09_2024/7ngl_12315_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngl_12315/09_2024/7ngl_12315_trim.cif" } resolution = 3.8 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= 0.003 sd= 0.039 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 162 5.16 5 C 23442 2.51 5 N 6426 2.21 5 O 6978 1.98 5 H 37715 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74735 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12429 Classifications: {'peptide': 776} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.97, per 1000 atoms: 0.35 Number of scatterers: 74735 At special positions: 0 Unit cell: (143.763, 146.256, 224.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 162 16.00 P 12 15.00 O 6978 8.00 N 6426 7.00 C 23442 6.00 H 37715 1.00 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.52 Conformation dependent library (CDL) restraints added in 4.6 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 41 sheets defined 52.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'A' and resid 148 through 156 removed outlier: 4.016A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.686A pdb=" N VAL A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.681A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.746A pdb=" N LEU A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 354 through 407 removed outlier: 3.563A pdb=" N ARG A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.580A pdb=" N ILE A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 removed outlier: 4.208A pdb=" N ASP A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 4.068A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.719A pdb=" N ALA A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 removed outlier: 3.690A pdb=" N LYS A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 554 through 560 removed outlier: 4.051A pdb=" N ILE A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.712A pdb=" N GLN A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.791A pdb=" N LYS A 594 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.889A pdb=" N ALA A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.660A pdb=" N ASN A 618 " --> pdb=" O GLN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 662 through 674 removed outlier: 3.998A pdb=" N LEU A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 692 through 703 removed outlier: 3.814A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 729 removed outlier: 3.886A pdb=" N SER A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.948A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 removed outlier: 4.028A pdb=" N MET A 826 " --> pdb=" O ARG A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Proline residue: A 854 - end of helix Processing helix chain 'A' and resid 856 through 870 removed outlier: 3.513A pdb=" N ILE A 860 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 862 " --> pdb=" O CYS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 removed outlier: 3.644A pdb=" N LYS A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.531A pdb=" N PHE A 920 " --> pdb=" O ASN A 916 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 916 through 921' Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 938 through 947 removed outlier: 4.402A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.983A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.772A pdb=" N VAL B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.838A pdb=" N ALA B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 removed outlier: 3.546A pdb=" N GLN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.693A pdb=" N LEU B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 removed outlier: 3.849A pdb=" N GLU B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 389 removed outlier: 3.602A pdb=" N ARG B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.996A pdb=" N LEU B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 removed outlier: 3.983A pdb=" N ILE B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.955A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.698A pdb=" N ALA B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.767A pdb=" N LYS B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 541 removed outlier: 3.713A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 560 removed outlier: 3.805A pdb=" N ILE B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 removed outlier: 3.500A pdb=" N GLN B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.895A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.687A pdb=" N ASN B 618 " --> pdb=" O GLN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 Processing helix chain 'B' and resid 662 through 674 removed outlier: 4.171A pdb=" N LEU B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 692 through 703 removed outlier: 3.814A pdb=" N LEU B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 729 removed outlier: 4.040A pdb=" N SER B 729 " --> pdb=" O TYR B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 747 removed outlier: 4.252A pdb=" N GLN B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 removed outlier: 3.594A pdb=" N MET B 826 " --> pdb=" O ARG B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Proline residue: B 854 - end of helix Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.583A pdb=" N ILE B 860 " --> pdb=" O ALA B 856 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.571A pdb=" N LYS B 898 " --> pdb=" O GLY B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 923 removed outlier: 3.859A pdb=" N TYR B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 923 " --> pdb=" O ASP B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 removed outlier: 3.621A pdb=" N THR B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 4.379A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 943 " --> pdb=" O TYR B 939 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 4.170A pdb=" N GLU C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.741A pdb=" N VAL C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 307 removed outlier: 3.553A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.592A pdb=" N GLN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 337 removed outlier: 3.552A pdb=" N LEU C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 removed outlier: 3.502A pdb=" N LEU C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 406 removed outlier: 3.599A pdb=" N LEU C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 428 Processing helix chain 'C' and resid 431 through 448 Processing helix chain 'C' and resid 452 through 468 removed outlier: 4.033A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 3.764A pdb=" N ALA C 483 " --> pdb=" O ASP C 479 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 removed outlier: 3.554A pdb=" N LYS C 498 " --> pdb=" O MET C 494 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 511 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 541 Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.862A pdb=" N ILE C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 removed outlier: 3.581A pdb=" N GLN C 575 " --> pdb=" O GLY C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.694A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.738A pdb=" N ASN C 618 " --> pdb=" O GLN C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 662 through 673 removed outlier: 3.979A pdb=" N LEU C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 692 through 703 removed outlier: 3.689A pdb=" N LEU C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 729 removed outlier: 3.578A pdb=" N SER C 729 " --> pdb=" O TYR C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 747 removed outlier: 3.967A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 removed outlier: 3.801A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Proline residue: C 854 - end of helix Processing helix chain 'C' and resid 856 through 870 removed outlier: 3.554A pdb=" N ILE C 860 " --> pdb=" O ALA C 856 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 removed outlier: 3.611A pdb=" N LYS C 898 " --> pdb=" O GLY C 894 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 905 " --> pdb=" O ALA C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 917 No H-bonds generated for 'chain 'C' and resid 915 through 917' Processing helix chain 'C' and resid 918 through 923 Processing helix chain 'C' and resid 924 through 929 removed outlier: 3.590A pdb=" N THR C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 947 removed outlier: 4.395A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 943 " --> pdb=" O TYR C 939 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 944 " --> pdb=" O ARG C 940 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 removed outlier: 3.801A pdb=" N GLU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 290 through 307 removed outlier: 3.620A pdb=" N ALA D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 removed outlier: 3.639A pdb=" N MET D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 removed outlier: 3.660A pdb=" N LEU D 331 " --> pdb=" O ASN D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 354 through 389 Processing helix chain 'D' and resid 391 through 406 removed outlier: 3.797A pdb=" N LEU D 395 " --> pdb=" O HIS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 428 removed outlier: 4.325A pdb=" N ILE D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.602A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 removed outlier: 3.876A pdb=" N ALA D 483 " --> pdb=" O ASP D 479 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 511 Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 571 through 581 removed outlier: 3.765A pdb=" N GLN D 575 " --> pdb=" O GLY D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.652A pdb=" N LYS D 594 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 607 Processing helix chain 'D' and resid 607 through 612 Processing helix chain 'D' and resid 614 through 619 Processing helix chain 'D' and resid 646 through 651 Processing helix chain 'D' and resid 662 through 674 removed outlier: 3.997A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 682 Processing helix chain 'D' and resid 692 through 703 removed outlier: 3.691A pdb=" N LEU D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 729 removed outlier: 3.676A pdb=" N SER D 729 " --> pdb=" O TYR D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 747 removed outlier: 4.479A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE D 745 " --> pdb=" O ASN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 removed outlier: 3.560A pdb=" N MET D 826 " --> pdb=" O ARG D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Proline residue: D 854 - end of helix Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.664A pdb=" N ILE D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 905 removed outlier: 3.791A pdb=" N LYS D 898 " --> pdb=" O GLY D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 917 No H-bonds generated for 'chain 'D' and resid 915 through 917' Processing helix chain 'D' and resid 918 through 923 Processing helix chain 'D' and resid 924 through 929 removed outlier: 3.525A pdb=" N THR D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 945 removed outlier: 3.631A pdb=" N PHE D 943 " --> pdb=" O TYR D 939 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP D 944 " --> pdb=" O ARG D 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 removed outlier: 3.687A pdb=" N GLU E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.818A pdb=" N VAL E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 307 Processing helix chain 'E' and resid 312 through 318 removed outlier: 3.575A pdb=" N GLN E 316 " --> pdb=" O GLU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 342 through 352 removed outlier: 3.545A pdb=" N LEU E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 404 removed outlier: 3.534A pdb=" N ARG E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 428 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.789A pdb=" N GLY E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 468 removed outlier: 3.731A pdb=" N ASN E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 468 " --> pdb=" O TRP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 490 removed outlier: 4.009A pdb=" N ALA E 483 " --> pdb=" O ASP E 479 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP E 490 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 512 removed outlier: 3.566A pdb=" N LYS E 498 " --> pdb=" O MET E 494 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG E 511 " --> pdb=" O VAL E 507 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY E 512 " --> pdb=" O SER E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 581 Processing helix chain 'E' and resid 591 through 595 Processing helix chain 'E' and resid 602 through 612 removed outlier: 3.571A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 608 " --> pdb=" O SER E 604 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 Processing helix chain 'E' and resid 646 through 653 removed outlier: 3.916A pdb=" N ARG E 652 " --> pdb=" O PRO E 648 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET E 653 " --> pdb=" O LEU E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 674 removed outlier: 4.252A pdb=" N ARG E 672 " --> pdb=" O ALA E 668 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 674 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 682 Processing helix chain 'E' and resid 692 through 703 removed outlier: 3.794A pdb=" N LEU E 696 " --> pdb=" O SER E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 729 removed outlier: 3.938A pdb=" N SER E 729 " --> pdb=" O TYR E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 747 removed outlier: 4.495A pdb=" N GLN E 743 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP E 744 " --> pdb=" O GLU E 740 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE E 745 " --> pdb=" O ASN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 removed outlier: 3.891A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 855 Proline residue: E 854 - end of helix Processing helix chain 'E' and resid 856 through 870 removed outlier: 3.638A pdb=" N ILE E 860 " --> pdb=" O ALA E 856 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 861 " --> pdb=" O GLY E 857 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR E 862 " --> pdb=" O CYS E 858 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 905 removed outlier: 3.728A pdb=" N LYS E 898 " --> pdb=" O GLY E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 915 through 917 No H-bonds generated for 'chain 'E' and resid 915 through 917' Processing helix chain 'E' and resid 918 through 923 Processing helix chain 'E' and resid 924 through 929 removed outlier: 3.690A pdb=" N THR E 928 " --> pdb=" O ALA E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 947 removed outlier: 4.237A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 156 removed outlier: 4.294A pdb=" N LEU F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 removed outlier: 3.807A pdb=" N VAL F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 307 removed outlier: 3.666A pdb=" N ALA F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.650A pdb=" N MET F 318 " --> pdb=" O VAL F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 removed outlier: 3.792A pdb=" N LEU F 331 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 removed outlier: 3.514A pdb=" N LEU F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 389 Processing helix chain 'F' and resid 391 through 405 removed outlier: 3.751A pdb=" N LEU F 395 " --> pdb=" O HIS F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 428 removed outlier: 4.271A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.844A pdb=" N GLY F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.930A pdb=" N ILE F 468 " --> pdb=" O TRP F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 490 removed outlier: 3.661A pdb=" N ALA F 483 " --> pdb=" O ASP F 479 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP F 490 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 509 removed outlier: 3.575A pdb=" N LYS F 498 " --> pdb=" O MET F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 541 Processing helix chain 'F' and resid 554 through 560 removed outlier: 3.949A pdb=" N ILE F 558 " --> pdb=" O ASP F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.601A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 595 Processing helix chain 'F' and resid 602 through 612 removed outlier: 3.884A pdb=" N ALA F 606 " --> pdb=" O ASP F 602 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU F 608 " --> pdb=" O SER F 604 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.670A pdb=" N ALA F 617 " --> pdb=" O GLU F 614 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN F 618 " --> pdb=" O GLN F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 651 removed outlier: 3.737A pdb=" N ASP F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 674 removed outlier: 4.072A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG F 672 " --> pdb=" O ALA F 668 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 674 " --> pdb=" O ALA F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 682 Processing helix chain 'F' and resid 685 through 687 No H-bonds generated for 'chain 'F' and resid 685 through 687' Processing helix chain 'F' and resid 692 through 703 removed outlier: 3.845A pdb=" N LEU F 696 " --> pdb=" O SER F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 729 removed outlier: 3.780A pdb=" N SER F 729 " --> pdb=" O TYR F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 747 removed outlier: 4.278A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 removed outlier: 4.083A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 849 through 855 Proline residue: F 854 - end of helix Processing helix chain 'F' and resid 856 through 870 removed outlier: 3.518A pdb=" N ILE F 860 " --> pdb=" O ALA F 856 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 861 " --> pdb=" O GLY F 857 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR F 862 " --> pdb=" O CYS F 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 905 removed outlier: 3.687A pdb=" N LYS F 898 " --> pdb=" O GLY F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 923 removed outlier: 3.844A pdb=" N TYR F 921 " --> pdb=" O LYS F 917 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP F 922 " --> pdb=" O LYS F 918 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU F 923 " --> pdb=" O ASP F 919 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 929 removed outlier: 3.608A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 938 through 947 removed outlier: 4.297A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP F 944 " --> pdb=" O ARG F 940 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE F 947 " --> pdb=" O PHE F 943 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 167 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.960A pdb=" N PHE A 545 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP A 590 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE A 547 " --> pdb=" O ASP A 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.828A pdb=" N LYS A 690 " --> pdb=" O VAL A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 766 removed outlier: 6.114A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AA9, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AB1, first strand: chain 'B' and resid 544 through 548 removed outlier: 7.007A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 689 through 691 removed outlier: 6.751A pdb=" N LYS B 690 " --> pdb=" O VAL B 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 764 through 766 removed outlier: 6.137A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 910 through 913 removed outlier: 6.698A pdb=" N ILE B 910 " --> pdb=" O HIS B 934 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL B 936 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU B 912 " --> pdb=" O VAL B 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'C' and resid 163 through 169 removed outlier: 6.626A pdb=" N VAL C 164 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR C 190 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 166 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR C 188 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU C 168 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 520 through 522 Processing sheet with id=AB8, first strand: chain 'C' and resid 544 through 548 removed outlier: 3.658A pdb=" N PHE C 545 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 689 through 691 removed outlier: 6.927A pdb=" N LYS C 690 " --> pdb=" O VAL C 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 764 through 766 removed outlier: 6.174A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 910 through 913 removed outlier: 6.738A pdb=" N ILE C 910 " --> pdb=" O HIS C 934 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 936 " --> pdb=" O ILE C 910 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU C 912 " --> pdb=" O VAL C 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AC4, first strand: chain 'D' and resid 163 through 167 Processing sheet with id=AC5, first strand: chain 'D' and resid 519 through 520 Processing sheet with id=AC6, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.245A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 764 through 766 removed outlier: 6.007A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 910 through 913 removed outlier: 6.889A pdb=" N ILE D 910 " --> pdb=" O HIS D 934 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL D 936 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU D 912 " --> pdb=" O VAL D 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AD1, first strand: chain 'E' and resid 164 through 167 Processing sheet with id=AD2, first strand: chain 'E' and resid 637 through 639 removed outlier: 6.002A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 543 through 548 removed outlier: 6.492A pdb=" N GLU E 543 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU E 588 " --> pdb=" O GLU E 543 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.888A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 764 through 765 removed outlier: 6.078A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 910 through 913 removed outlier: 6.682A pdb=" N ILE E 910 " --> pdb=" O HIS E 934 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL E 936 " --> pdb=" O ILE E 910 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU E 912 " --> pdb=" O VAL E 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AD8, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.360A pdb=" N VAL F 164 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA F 192 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU F 168 " --> pdb=" O TYR F 186 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.360A pdb=" N VAL F 164 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA F 192 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 634 through 639 removed outlier: 3.524A pdb=" N PHE F 635 " --> pdb=" O LYS F 517 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ILE F 656 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS F 520 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.975A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.972A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 764 through 769 removed outlier: 6.143A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 878 through 879 removed outlier: 7.412A pdb=" N ALA F 878 " --> pdb=" O VAL F 911 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE F 910 " --> pdb=" O HIS F 934 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 936 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU F 912 " --> pdb=" O VAL F 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 1532 hydrogen bonds defined for protein. 4395 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: 26.92 Time building geometry restraints manager: 17.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 37673 1.02 - 1.22: 159 1.22 - 1.42: 14911 1.42 - 1.62: 22333 1.62 - 1.82: 283 Bond restraints: 75359 Sorted by residual: bond pdb=" CG GLU E 665 " pdb=" CD GLU E 665 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.34e+01 bond pdb=" CG GLU A 665 " pdb=" CD GLU A 665 " ideal model delta sigma weight residual 1.516 1.427 0.089 2.50e-02 1.60e+03 1.28e+01 bond pdb=" CG GLU C 665 " pdb=" CD GLU C 665 " ideal model delta sigma weight residual 1.516 1.428 0.088 2.50e-02 1.60e+03 1.25e+01 bond pdb=" CG GLU B 665 " pdb=" CD GLU B 665 " ideal model delta sigma weight residual 1.516 1.433 0.083 2.50e-02 1.60e+03 1.11e+01 bond pdb=" CB ILE D 403 " pdb=" CG2 ILE D 403 " ideal model delta sigma weight residual 1.521 1.629 -0.108 3.30e-02 9.18e+02 1.07e+01 ... (remaining 75354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 133891 3.76 - 7.52: 2969 7.52 - 11.28: 96 11.28 - 15.03: 12 15.03 - 18.79: 3 Bond angle restraints: 136971 Sorted by residual: angle pdb=" N GLY F 601 " pdb=" CA GLY F 601 " pdb=" C GLY F 601 " ideal model delta sigma weight residual 113.18 94.39 18.79 2.37e+00 1.78e-01 6.29e+01 angle pdb=" N GLY D 601 " pdb=" CA GLY D 601 " pdb=" C GLY D 601 " ideal model delta sigma weight residual 113.18 95.96 17.22 2.37e+00 1.78e-01 5.28e+01 angle pdb=" N GLY E 601 " pdb=" CA GLY E 601 " pdb=" C GLY E 601 " ideal model delta sigma weight residual 113.18 97.91 15.27 2.37e+00 1.78e-01 4.15e+01 angle pdb=" N GLY C 601 " pdb=" CA GLY C 601 " pdb=" C GLY C 601 " ideal model delta sigma weight residual 113.18 98.76 14.42 2.37e+00 1.78e-01 3.70e+01 angle pdb=" N GLY B 210 " pdb=" CA GLY B 210 " pdb=" C GLY B 210 " ideal model delta sigma weight residual 113.18 100.17 13.01 2.37e+00 1.78e-01 3.01e+01 ... (remaining 136966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 33809 31.27 - 62.53: 1033 62.53 - 93.80: 62 93.80 - 125.07: 1 125.07 - 156.34: 3 Dihedral angle restraints: 34908 sinusoidal: 19668 harmonic: 15240 Sorted by residual: dihedral pdb=" O1B ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PB ADP D1001 " pdb=" PA ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 143.66 156.34 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 69.25 -129.25 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 66.43 -126.43 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 34905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4739 0.093 - 0.185: 1015 0.185 - 0.278: 70 0.278 - 0.371: 6 0.371 - 0.463: 2 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CB ILE D 558 " pdb=" CA ILE D 558 " pdb=" CG1 ILE D 558 " pdb=" CG2 ILE D 558 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CG LEU C 462 " pdb=" CB LEU C 462 " pdb=" CD1 LEU C 462 " pdb=" CD2 LEU C 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 5829 not shown) Planarity restraints: 10980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 491 " -0.038 2.00e-02 2.50e+03 3.41e-02 2.62e+01 pdb=" CG HIS E 491 " 0.085 2.00e-02 2.50e+03 pdb=" ND1 HIS E 491 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS E 491 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS E 491 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS E 491 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 HIS E 491 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 HIS E 491 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS E 491 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 615 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C GLN E 615 " -0.083 2.00e-02 2.50e+03 pdb=" O GLN E 615 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN E 616 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 861 " -0.024 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C VAL D 861 " 0.082 2.00e-02 2.50e+03 pdb=" O VAL D 861 " -0.031 2.00e-02 2.50e+03 pdb=" N THR D 862 " -0.028 2.00e-02 2.50e+03 ... (remaining 10977 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 7209 2.23 - 2.82: 162213 2.82 - 3.41: 193128 3.41 - 4.01: 243299 4.01 - 4.60: 381966 Nonbonded interactions: 987815 Sorted by model distance: nonbonded pdb=" O GLU E 543 " pdb=" H LEU E 586 " model vdw 1.636 2.450 nonbonded pdb=" O PHE C 619 " pdb=" H VAL C 628 " model vdw 1.649 2.450 nonbonded pdb=" O ASP B 852 " pdb=" HG SER B 855 " model vdw 1.651 2.450 nonbonded pdb=" OD1 ASP F 415 " pdb="HH12 ARG F 422 " model vdw 1.667 2.450 nonbonded pdb=" O CYS C 576 " pdb=" HG1 THR C 580 " model vdw 1.668 2.450 ... (remaining 987810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'B' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'C' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'D' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = chain 'E' selection = (chain 'F' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) } 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=0.00 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: 3.570 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: 0.940 Extract box with map and model: 2.140 Check model and map are aligned: 0.430 Set scattering table: 0.510 Process input model: 119.490 Find NCS groups from input model: 2.500 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: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.012 0.134 37644 Z= 0.763 Angle : 1.497 18.792 50856 Z= 0.830 Chirality : 0.072 0.463 5832 Planarity : 0.009 0.055 6528 Dihedral : 13.267 156.335 14466 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.22 % Favored : 90.76 % Rotamer: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.12), residues: 4632 helix: -2.07 (0.09), residues: 1874 sheet: -3.71 (0.18), residues: 567 loop : -0.47 (0.15), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.006 TRP D 464 HIS 0.051 0.004 HIS E 491 PHE 0.049 0.005 PHE E 504 TYR 0.041 0.005 TYR C 623 ARG 0.017 0.001 ARG D 786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 4.354 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: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.0070 (mtp) cc_final: -0.0179 (mmm) REVERT: A 206 MET cc_start: 0.4321 (ttp) cc_final: 0.3916 (tmm) REVERT: A 317 MET cc_start: 0.1116 (mmp) cc_final: 0.0023 (ptt) REVERT: A 651 ASP cc_start: 0.8101 (t0) cc_final: 0.7857 (t0) REVERT: A 773 MET cc_start: 0.8674 (ppp) cc_final: 0.8167 (ppp) REVERT: B 317 MET cc_start: 0.3181 (mmp) cc_final: 0.2907 (mtt) REVERT: B 490 ASP cc_start: 0.8184 (p0) cc_final: 0.7502 (t0) REVERT: B 496 ASP cc_start: 0.8181 (t0) cc_final: 0.7757 (t0) REVERT: B 773 MET cc_start: 0.8212 (ppp) cc_final: 0.7898 (ppp) REVERT: C 197 MET cc_start: 0.2022 (mtp) cc_final: 0.1553 (pmm) REVERT: C 488 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7448 (tt0) REVERT: C 543 GLU cc_start: 0.6207 (tm-30) cc_final: 0.5902 (mt-10) REVERT: D 327 ASN cc_start: 0.7266 (m-40) cc_final: 0.6982 (t0) REVERT: D 397 GLN cc_start: 0.7896 (mt0) cc_final: 0.7518 (tp40) REVERT: D 653 MET cc_start: 0.6111 (ptm) cc_final: 0.5854 (ptm) REVERT: D 756 MET cc_start: 0.5772 (mpp) cc_final: 0.5249 (ptm) REVERT: D 773 MET cc_start: 0.5128 (mmm) cc_final: 0.4318 (mpp) REVERT: D 810 MET cc_start: 0.8795 (mmt) cc_final: 0.8230 (mtt) REVERT: E 406 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7663 (pp20) REVERT: E 655 MET cc_start: 0.7735 (mpp) cc_final: 0.7441 (mmm) REVERT: E 685 ASP cc_start: 0.8323 (t0) cc_final: 0.7511 (p0) REVERT: E 896 LYS cc_start: 0.6784 (tttt) cc_final: 0.6580 (tttt) REVERT: F 272 MET cc_start: 0.0654 (ptp) cc_final: 0.0450 (ptp) REVERT: F 609 GLU cc_start: 0.8588 (pt0) cc_final: 0.8222 (tp30) outliers start: 1 outliers final: 1 residues processed: 397 average time/residue: 1.0080 time to fit residues: 643.8252 Evaluate side-chains 245 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 362 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 419 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 916 ASN E 876 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37644 Z= 0.212 Angle : 0.686 7.286 50856 Z= 0.358 Chirality : 0.042 0.166 5832 Planarity : 0.005 0.060 6528 Dihedral : 7.208 154.532 5132 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.42 % Allowed : 8.00 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.12), residues: 4632 helix: -0.59 (0.11), residues: 1999 sheet: -3.39 (0.18), residues: 603 loop : -1.01 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 464 HIS 0.016 0.001 HIS F 433 PHE 0.019 0.001 PHE F 191 TYR 0.028 0.001 TYR A 360 ARG 0.007 0.001 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 269 time to evaluate : 4.442 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: A 197 MET cc_start: -0.0206 (mtp) cc_final: -0.0409 (mmm) REVERT: A 206 MET cc_start: 0.4554 (ttp) cc_final: 0.4297 (tpp) REVERT: A 317 MET cc_start: 0.1132 (mmp) cc_final: -0.0156 (ttp) REVERT: A 318 MET cc_start: -0.4787 (mtm) cc_final: -0.5047 (mtp) REVERT: A 543 GLU cc_start: 0.7690 (mp0) cc_final: 0.7267 (mp0) REVERT: A 773 MET cc_start: 0.8624 (ppp) cc_final: 0.8052 (ppp) REVERT: B 490 ASP cc_start: 0.8106 (p0) cc_final: 0.7630 (t0) REVERT: B 665 GLU cc_start: 0.7641 (tp30) cc_final: 0.7208 (tm-30) REVERT: B 741 ASN cc_start: 0.8001 (t0) cc_final: 0.7780 (t0) REVERT: B 773 MET cc_start: 0.8168 (ppp) cc_final: 0.7915 (ppp) REVERT: C 197 MET cc_start: 0.2086 (mtp) cc_final: 0.1649 (pmm) REVERT: C 543 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5923 (mt-10) REVERT: C 806 LEU cc_start: 0.7977 (pt) cc_final: 0.7643 (pp) REVERT: D 327 ASN cc_start: 0.7279 (m-40) cc_final: 0.7017 (t0) REVERT: D 397 GLN cc_start: 0.7987 (mt0) cc_final: 0.7565 (tp40) REVERT: D 756 MET cc_start: 0.5977 (mpp) cc_final: 0.5656 (ptm) REVERT: D 773 MET cc_start: 0.4771 (mmm) cc_final: 0.4143 (mpp) REVERT: D 810 MET cc_start: 0.8790 (mmt) cc_final: 0.8210 (mtt) REVERT: E 406 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7687 (pp20) REVERT: E 441 GLU cc_start: 0.6269 (mm-30) cc_final: 0.5826 (mt-10) REVERT: E 653 MET cc_start: 0.7949 (pmm) cc_final: 0.6863 (pmm) REVERT: E 655 MET cc_start: 0.7586 (mpp) cc_final: 0.7251 (mpp) REVERT: E 685 ASP cc_start: 0.8199 (t0) cc_final: 0.7693 (p0) REVERT: E 731 GLU cc_start: 0.7054 (mp0) cc_final: 0.6184 (pm20) REVERT: E 783 SER cc_start: 0.9018 (t) cc_final: 0.8637 (p) REVERT: F 272 MET cc_start: 0.0289 (ptp) cc_final: 0.0033 (ptp) REVERT: F 609 GLU cc_start: 0.8437 (pt0) cc_final: 0.7859 (mm-30) REVERT: F 671 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7824 (tm-30) outliers start: 17 outliers final: 13 residues processed: 280 average time/residue: 0.9279 time to fit residues: 426.9566 Evaluate side-chains 242 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 229 time to evaluate : 4.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 895 ILE Chi-restraints excluded: chain D residue 828 HIS Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 908 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 115 optimal weight: 0.0010 chunk 420 optimal weight: 0.1980 chunk 454 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 416 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 overall best weight: 1.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 HIS ** A 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37644 Z= 0.192 Angle : 0.595 7.965 50856 Z= 0.302 Chirality : 0.040 0.155 5832 Planarity : 0.004 0.047 6528 Dihedral : 6.666 139.838 5132 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.40 % Allowed : 9.14 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.12), residues: 4632 helix: 0.14 (0.11), residues: 2019 sheet: -3.14 (0.20), residues: 595 loop : -1.13 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 770 HIS 0.008 0.001 HIS F 433 PHE 0.015 0.001 PHE B 421 TYR 0.025 0.001 TYR A 360 ARG 0.006 0.000 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 244 time to evaluate : 4.363 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: A 197 MET cc_start: -0.0161 (mtp) cc_final: -0.0579 (mmt) REVERT: A 206 MET cc_start: 0.4550 (ttp) cc_final: 0.4313 (tpp) REVERT: A 317 MET cc_start: 0.1060 (mmp) cc_final: -0.0188 (ttp) REVERT: A 773 MET cc_start: 0.8642 (ppp) cc_final: 0.8039 (ppp) REVERT: B 490 ASP cc_start: 0.8140 (p0) cc_final: 0.7793 (t0) REVERT: B 741 ASN cc_start: 0.7932 (t0) cc_final: 0.7701 (t0) REVERT: B 773 MET cc_start: 0.8143 (ppp) cc_final: 0.7855 (ppp) REVERT: C 543 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5867 (mt-10) REVERT: C 806 LEU cc_start: 0.7982 (pt) cc_final: 0.7630 (pp) REVERT: D 327 ASN cc_start: 0.7252 (m-40) cc_final: 0.6977 (t0) REVERT: D 397 GLN cc_start: 0.8031 (mt0) cc_final: 0.7634 (tp40) REVERT: D 637 CYS cc_start: 0.8981 (m) cc_final: 0.8780 (t) REVERT: D 756 MET cc_start: 0.5890 (mpp) cc_final: 0.5543 (ptm) REVERT: D 773 MET cc_start: 0.4670 (mmm) cc_final: 0.4046 (mpp) REVERT: D 810 MET cc_start: 0.8820 (mmt) cc_final: 0.8213 (mtt) REVERT: D 879 MET cc_start: 0.6969 (pmm) cc_final: 0.6764 (pmm) REVERT: E 406 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7719 (pp20) REVERT: E 653 MET cc_start: 0.7777 (pmm) cc_final: 0.6539 (pmm) REVERT: E 655 MET cc_start: 0.7522 (mpp) cc_final: 0.7148 (mpp) REVERT: E 685 ASP cc_start: 0.8264 (t0) cc_final: 0.7698 (p0) REVERT: E 783 SER cc_start: 0.8997 (t) cc_final: 0.8662 (p) REVERT: F 435 MET cc_start: 0.8428 (tmm) cc_final: 0.8134 (tmm) REVERT: F 609 GLU cc_start: 0.8334 (pt0) cc_final: 0.7977 (tp30) REVERT: F 671 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7832 (tm-30) outliers start: 16 outliers final: 13 residues processed: 254 average time/residue: 0.9181 time to fit residues: 381.0482 Evaluate side-chains 230 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 828 HIS Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain E residue 908 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 421 optimal weight: 1.9990 chunk 446 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 399 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37644 Z= 0.224 Angle : 0.574 7.289 50856 Z= 0.290 Chirality : 0.039 0.151 5832 Planarity : 0.004 0.042 6528 Dihedral : 6.514 136.846 5132 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.67 % Allowed : 9.75 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.12), residues: 4632 helix: 0.43 (0.11), residues: 2036 sheet: -2.93 (0.21), residues: 567 loop : -1.33 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 770 HIS 0.008 0.001 HIS F 433 PHE 0.029 0.001 PHE B 421 TYR 0.026 0.001 TYR E 394 ARG 0.011 0.000 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 4.376 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: A 197 MET cc_start: -0.0192 (mtp) cc_final: -0.0795 (mmt) REVERT: A 206 MET cc_start: 0.4483 (ttp) cc_final: 0.4008 (tmm) REVERT: A 317 MET cc_start: 0.1195 (mmp) cc_final: 0.0822 (tpt) REVERT: A 773 MET cc_start: 0.8666 (ppp) cc_final: 0.8075 (ppp) REVERT: B 490 ASP cc_start: 0.8231 (p0) cc_final: 0.7945 (t70) REVERT: B 741 ASN cc_start: 0.7858 (t0) cc_final: 0.7593 (t0) REVERT: B 773 MET cc_start: 0.8155 (ppp) cc_final: 0.7861 (ppp) REVERT: C 806 LEU cc_start: 0.8010 (pt) cc_final: 0.7607 (pp) REVERT: D 327 ASN cc_start: 0.7254 (m-40) cc_final: 0.6980 (t0) REVERT: D 397 GLN cc_start: 0.8037 (mt0) cc_final: 0.7632 (tp40) REVERT: D 536 ILE cc_start: 0.8225 (mt) cc_final: 0.7922 (tp) REVERT: D 637 CYS cc_start: 0.9013 (m) cc_final: 0.8786 (t) REVERT: D 756 MET cc_start: 0.6077 (mpp) cc_final: 0.5762 (ptm) REVERT: D 773 MET cc_start: 0.4681 (mmm) cc_final: 0.4111 (mpp) REVERT: D 810 MET cc_start: 0.8855 (mmt) cc_final: 0.8293 (mtt) REVERT: D 879 MET cc_start: 0.7028 (pmm) cc_final: 0.6806 (pmm) REVERT: E 406 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7687 (pp20) REVERT: E 441 GLU cc_start: 0.6255 (mm-30) cc_final: 0.5829 (mt-10) REVERT: E 685 ASP cc_start: 0.8347 (t0) cc_final: 0.7747 (p0) REVERT: E 783 SER cc_start: 0.8963 (t) cc_final: 0.8662 (p) REVERT: F 435 MET cc_start: 0.8477 (tmm) cc_final: 0.8095 (tmm) REVERT: F 609 GLU cc_start: 0.8331 (pt0) cc_final: 0.8019 (mm-30) REVERT: F 671 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7851 (tm-30) outliers start: 27 outliers final: 21 residues processed: 252 average time/residue: 0.9662 time to fit residues: 404.7745 Evaluate side-chains 237 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 908 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 2.9990 chunk 253 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 332 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 381 optimal weight: 3.9990 chunk 308 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 0.7980 chunk 400 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN B 477 ASN C 277 ASN D 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37644 Z= 0.215 Angle : 0.558 7.521 50856 Z= 0.281 Chirality : 0.039 0.150 5832 Planarity : 0.003 0.041 6528 Dihedral : 6.378 130.667 5132 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.74 % Allowed : 10.32 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 4632 helix: 0.60 (0.11), residues: 2041 sheet: -2.89 (0.21), residues: 578 loop : -1.31 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 770 HIS 0.005 0.001 HIS F 433 PHE 0.024 0.001 PHE B 421 TYR 0.020 0.001 TYR A 360 ARG 0.005 0.000 ARG E 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 4.797 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: A 197 MET cc_start: -0.0113 (mtp) cc_final: -0.0743 (mmt) REVERT: A 206 MET cc_start: 0.4534 (ttp) cc_final: 0.4062 (tmm) REVERT: A 317 MET cc_start: 0.1297 (mmp) cc_final: 0.0916 (tpt) REVERT: A 773 MET cc_start: 0.8687 (ppp) cc_final: 0.8126 (ppp) REVERT: B 490 ASP cc_start: 0.8294 (p0) cc_final: 0.7946 (t70) REVERT: B 741 ASN cc_start: 0.7797 (t0) cc_final: 0.7554 (t0) REVERT: B 773 MET cc_start: 0.8140 (ppp) cc_final: 0.7839 (ppp) REVERT: C 806 LEU cc_start: 0.8010 (pt) cc_final: 0.7742 (pp) REVERT: D 327 ASN cc_start: 0.7236 (m-40) cc_final: 0.6958 (t0) REVERT: D 397 GLN cc_start: 0.8036 (mt0) cc_final: 0.7628 (tp40) REVERT: D 536 ILE cc_start: 0.8208 (mt) cc_final: 0.7902 (tp) REVERT: D 637 CYS cc_start: 0.9078 (m) cc_final: 0.8848 (t) REVERT: D 756 MET cc_start: 0.6074 (mpp) cc_final: 0.5859 (ptm) REVERT: D 773 MET cc_start: 0.4596 (mmm) cc_final: 0.4129 (mpp) REVERT: D 810 MET cc_start: 0.8835 (mmt) cc_final: 0.8312 (mtt) REVERT: D 879 MET cc_start: 0.7093 (pmm) cc_final: 0.6881 (pmm) REVERT: E 406 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7709 (pp20) REVERT: E 441 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5839 (mt-10) REVERT: E 685 ASP cc_start: 0.8313 (t0) cc_final: 0.7762 (p0) REVERT: E 783 SER cc_start: 0.8972 (t) cc_final: 0.8696 (p) REVERT: F 435 MET cc_start: 0.8481 (tmm) cc_final: 0.8098 (tmm) REVERT: F 671 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7886 (tm-30) outliers start: 30 outliers final: 23 residues processed: 243 average time/residue: 0.8934 time to fit residues: 367.5137 Evaluate side-chains 229 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 1.9990 chunk 402 optimal weight: 20.0000 chunk 88 optimal weight: 0.3980 chunk 262 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 447 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 147 optimal weight: 0.0040 chunk 234 optimal weight: 8.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 37644 Z= 0.156 Angle : 0.529 7.065 50856 Z= 0.263 Chirality : 0.038 0.152 5832 Planarity : 0.003 0.039 6528 Dihedral : 6.210 127.995 5132 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.64 % Allowed : 10.64 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 4632 helix: 0.79 (0.12), residues: 2050 sheet: -2.65 (0.21), residues: 574 loop : -1.30 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 770 HIS 0.006 0.001 HIS F 433 PHE 0.026 0.001 PHE B 421 TYR 0.017 0.001 TYR A 360 ARG 0.004 0.000 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 4.348 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: A 197 MET cc_start: 0.0006 (mtp) cc_final: -0.0641 (mmt) REVERT: A 206 MET cc_start: 0.4533 (ttp) cc_final: 0.4058 (tmm) REVERT: A 317 MET cc_start: 0.1329 (mmp) cc_final: 0.0936 (tpt) REVERT: A 773 MET cc_start: 0.8690 (ppp) cc_final: 0.8125 (ppp) REVERT: B 490 ASP cc_start: 0.8344 (p0) cc_final: 0.7943 (t70) REVERT: B 741 ASN cc_start: 0.7728 (t0) cc_final: 0.7517 (t0) REVERT: B 773 MET cc_start: 0.8134 (ppp) cc_final: 0.7837 (ppp) REVERT: C 433 HIS cc_start: 0.7876 (t70) cc_final: 0.7419 (p90) REVERT: C 806 LEU cc_start: 0.7988 (pt) cc_final: 0.7715 (pp) REVERT: D 327 ASN cc_start: 0.7153 (m-40) cc_final: 0.6858 (t0) REVERT: D 397 GLN cc_start: 0.7991 (mt0) cc_final: 0.7591 (tp40) REVERT: D 536 ILE cc_start: 0.8203 (mt) cc_final: 0.7921 (tp) REVERT: D 773 MET cc_start: 0.4508 (mmm) cc_final: 0.4075 (mpp) REVERT: D 810 MET cc_start: 0.8812 (mmt) cc_final: 0.8347 (mtt) REVERT: D 879 MET cc_start: 0.7163 (pmm) cc_final: 0.6931 (pmm) REVERT: E 406 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7639 (pp20) REVERT: E 435 MET cc_start: 0.7750 (mmt) cc_final: 0.7387 (tpt) REVERT: E 441 GLU cc_start: 0.6302 (mm-30) cc_final: 0.5932 (mt-10) REVERT: E 685 ASP cc_start: 0.8256 (t0) cc_final: 0.7755 (p0) REVERT: E 783 SER cc_start: 0.8954 (t) cc_final: 0.8715 (p) REVERT: F 272 MET cc_start: 0.0681 (ptp) cc_final: 0.0170 (ptp) REVERT: F 435 MET cc_start: 0.8474 (tmm) cc_final: 0.8072 (tmm) REVERT: F 671 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7852 (tm-30) outliers start: 26 outliers final: 19 residues processed: 236 average time/residue: 0.9049 time to fit residues: 359.7345 Evaluate side-chains 224 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 205 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 326 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 chunk 376 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 445 optimal weight: 2.9990 chunk 278 optimal weight: 20.0000 chunk 271 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37644 Z= 0.266 Angle : 0.569 6.807 50856 Z= 0.286 Chirality : 0.039 0.163 5832 Planarity : 0.003 0.041 6528 Dihedral : 6.237 125.897 5132 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.72 % Allowed : 11.26 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4632 helix: 0.76 (0.11), residues: 2046 sheet: -2.66 (0.21), residues: 565 loop : -1.35 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 470 HIS 0.005 0.001 HIS F 433 PHE 0.016 0.001 PHE F 947 TYR 0.031 0.001 TYR E 473 ARG 0.005 0.000 ARG E 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 4.360 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: A 197 MET cc_start: 0.0097 (mtp) cc_final: -0.0590 (mmt) REVERT: A 206 MET cc_start: 0.4525 (ttp) cc_final: 0.4053 (tmm) REVERT: A 317 MET cc_start: 0.1232 (mmp) cc_final: 0.0851 (tpt) REVERT: A 773 MET cc_start: 0.8738 (ppp) cc_final: 0.8170 (ppp) REVERT: B 569 MET cc_start: 0.8476 (tpp) cc_final: 0.7569 (mmm) REVERT: B 773 MET cc_start: 0.8164 (ppp) cc_final: 0.7849 (ppp) REVERT: C 433 HIS cc_start: 0.7893 (t70) cc_final: 0.7412 (p90) REVERT: C 806 LEU cc_start: 0.8160 (pt) cc_final: 0.7918 (pp) REVERT: D 327 ASN cc_start: 0.7152 (m-40) cc_final: 0.6866 (t0) REVERT: D 397 GLN cc_start: 0.7967 (mt0) cc_final: 0.7571 (tp40) REVERT: D 482 ARG cc_start: 0.7916 (tmt170) cc_final: 0.7653 (tpt-90) REVERT: D 536 ILE cc_start: 0.8212 (mt) cc_final: 0.7894 (tp) REVERT: D 773 MET cc_start: 0.4543 (mmm) cc_final: 0.4177 (mpp) REVERT: D 810 MET cc_start: 0.8814 (mmt) cc_final: 0.8365 (mtt) REVERT: D 879 MET cc_start: 0.7179 (pmm) cc_final: 0.6910 (pmm) REVERT: E 406 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7650 (pp20) REVERT: E 435 MET cc_start: 0.7775 (mmt) cc_final: 0.7410 (tpt) REVERT: E 441 GLU cc_start: 0.6298 (mm-30) cc_final: 0.5936 (mt-10) REVERT: E 653 MET cc_start: 0.7389 (pmm) cc_final: 0.6504 (pmm) REVERT: E 655 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6550 (mmm) REVERT: E 685 ASP cc_start: 0.8339 (t0) cc_final: 0.7768 (p0) REVERT: E 783 SER cc_start: 0.8963 (t) cc_final: 0.8702 (p) REVERT: F 272 MET cc_start: 0.0957 (ptp) cc_final: 0.0375 (ptp) REVERT: F 671 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7919 (tm-30) outliers start: 29 outliers final: 24 residues processed: 224 average time/residue: 0.9166 time to fit residues: 346.4237 Evaluate side-chains 224 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 134 optimal weight: 0.0870 chunk 87 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 303 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 350 optimal weight: 8.9990 overall best weight: 2.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37644 Z= 0.236 Angle : 0.558 10.265 50856 Z= 0.280 Chirality : 0.039 0.179 5832 Planarity : 0.003 0.042 6528 Dihedral : 6.217 123.349 5132 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.74 % Allowed : 11.75 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.12), residues: 4632 helix: 0.84 (0.12), residues: 2051 sheet: -2.59 (0.21), residues: 578 loop : -1.37 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 770 HIS 0.005 0.001 HIS F 433 PHE 0.024 0.001 PHE B 421 TYR 0.017 0.001 TYR A 360 ARG 0.004 0.000 ARG E 652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 4.397 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: A 197 MET cc_start: 0.0071 (mtp) cc_final: -0.0589 (mmt) REVERT: A 206 MET cc_start: 0.4510 (ttp) cc_final: 0.4050 (tmm) REVERT: A 317 MET cc_start: 0.1234 (mmp) cc_final: 0.0859 (tpt) REVERT: A 424 ARG cc_start: 0.8926 (mtt-85) cc_final: 0.8254 (ttp-110) REVERT: A 536 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8049 (tp) REVERT: A 773 MET cc_start: 0.8729 (ppp) cc_final: 0.8208 (ppp) REVERT: B 569 MET cc_start: 0.8477 (tpp) cc_final: 0.7568 (mmm) REVERT: B 766 MET cc_start: 0.8208 (mtp) cc_final: 0.7872 (mtp) REVERT: B 773 MET cc_start: 0.8188 (ppp) cc_final: 0.7885 (ppp) REVERT: C 433 HIS cc_start: 0.7896 (t70) cc_final: 0.7410 (p90) REVERT: C 806 LEU cc_start: 0.8119 (pt) cc_final: 0.7852 (pp) REVERT: D 327 ASN cc_start: 0.7138 (m-40) cc_final: 0.6847 (t0) REVERT: D 397 GLN cc_start: 0.7968 (mt0) cc_final: 0.7574 (tp40) REVERT: D 482 ARG cc_start: 0.7941 (tmt170) cc_final: 0.7675 (tpt-90) REVERT: D 536 ILE cc_start: 0.8197 (mt) cc_final: 0.7880 (tp) REVERT: D 773 MET cc_start: 0.4463 (mmm) cc_final: 0.4092 (mpp) REVERT: D 810 MET cc_start: 0.8806 (mmt) cc_final: 0.8369 (mtt) REVERT: D 879 MET cc_start: 0.7292 (pmm) cc_final: 0.6985 (pmm) REVERT: E 406 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7622 (pp20) REVERT: E 435 MET cc_start: 0.7785 (mmt) cc_final: 0.7416 (tpt) REVERT: E 441 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5924 (mt-10) REVERT: E 685 ASP cc_start: 0.8321 (t0) cc_final: 0.7777 (p0) REVERT: E 783 SER cc_start: 0.8951 (t) cc_final: 0.8675 (p) REVERT: F 435 MET cc_start: 0.8394 (tmm) cc_final: 0.8047 (ttm) REVERT: F 671 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7915 (tm-30) outliers start: 30 outliers final: 26 residues processed: 221 average time/residue: 0.9177 time to fit residues: 341.8370 Evaluate side-chains 224 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 637 CYS Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 20.0000 chunk 426 optimal weight: 0.9980 chunk 389 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 374 optimal weight: 5.9990 chunk 392 optimal weight: 9.9990 chunk 413 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37644 Z= 0.265 Angle : 0.566 6.865 50856 Z= 0.284 Chirality : 0.039 0.147 5832 Planarity : 0.004 0.042 6528 Dihedral : 6.197 118.695 5132 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.79 % Allowed : 11.93 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.12), residues: 4632 helix: 0.87 (0.12), residues: 2050 sheet: -2.57 (0.21), residues: 571 loop : -1.39 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 770 HIS 0.005 0.001 HIS D 561 PHE 0.019 0.001 PHE F 947 TYR 0.017 0.001 TYR A 360 ARG 0.005 0.000 ARG D 562 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 4.464 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: A 197 MET cc_start: 0.0180 (mtp) cc_final: -0.0536 (mmt) REVERT: A 206 MET cc_start: 0.4498 (ttp) cc_final: 0.4031 (tmm) REVERT: A 317 MET cc_start: 0.1203 (mmp) cc_final: 0.0835 (tpt) REVERT: A 536 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 773 MET cc_start: 0.8746 (ppp) cc_final: 0.8273 (ppp) REVERT: B 766 MET cc_start: 0.8248 (mtp) cc_final: 0.7898 (mtp) REVERT: B 773 MET cc_start: 0.8215 (ppp) cc_final: 0.7918 (ppp) REVERT: C 433 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7382 (p90) REVERT: C 552 MET cc_start: 0.7663 (ppp) cc_final: 0.7335 (ppp) REVERT: C 806 LEU cc_start: 0.8102 (pt) cc_final: 0.7676 (pp) REVERT: D 327 ASN cc_start: 0.7095 (m-40) cc_final: 0.6802 (t0) REVERT: D 397 GLN cc_start: 0.7969 (mt0) cc_final: 0.7583 (tp40) REVERT: D 536 ILE cc_start: 0.8197 (mt) cc_final: 0.7878 (tp) REVERT: D 773 MET cc_start: 0.4349 (mmm) cc_final: 0.4054 (mpp) REVERT: D 810 MET cc_start: 0.8810 (mmt) cc_final: 0.8401 (mtt) REVERT: D 879 MET cc_start: 0.7399 (pmm) cc_final: 0.7097 (pmm) REVERT: E 435 MET cc_start: 0.7806 (mmt) cc_final: 0.7443 (tpt) REVERT: E 441 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5927 (mt-10) REVERT: E 653 MET cc_start: 0.7345 (pmm) cc_final: 0.6439 (pmm) REVERT: E 685 ASP cc_start: 0.8341 (t0) cc_final: 0.7713 (p0) REVERT: E 783 SER cc_start: 0.8944 (t) cc_final: 0.8668 (p) REVERT: F 671 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7915 (tm-30) outliers start: 32 outliers final: 27 residues processed: 223 average time/residue: 0.9232 time to fit residues: 346.4460 Evaluate side-chains 227 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 637 CYS Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 8.9990 chunk 438 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 460 optimal weight: 3.9990 chunk 423 optimal weight: 10.0000 chunk 366 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 224 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37644 Z= 0.258 Angle : 0.567 9.829 50856 Z= 0.285 Chirality : 0.039 0.147 5832 Planarity : 0.004 0.063 6528 Dihedral : 6.169 115.336 5130 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.74 % Allowed : 12.07 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4632 helix: 0.90 (0.12), residues: 2052 sheet: -2.52 (0.21), residues: 566 loop : -1.42 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 470 HIS 0.005 0.001 HIS F 433 PHE 0.025 0.001 PHE C 421 TYR 0.016 0.001 TYR A 360 ARG 0.004 0.000 ARG E 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 4.333 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: A 197 MET cc_start: 0.0172 (mtp) cc_final: -0.0496 (mmt) REVERT: A 206 MET cc_start: 0.4496 (ttp) cc_final: 0.4030 (tmm) REVERT: A 317 MET cc_start: 0.1181 (mmp) cc_final: 0.0701 (tpt) REVERT: A 536 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8002 (tp) REVERT: A 773 MET cc_start: 0.8782 (ppp) cc_final: 0.8340 (ppp) REVERT: B 766 MET cc_start: 0.8210 (mtp) cc_final: 0.7897 (mtp) REVERT: B 773 MET cc_start: 0.8213 (ppp) cc_final: 0.7896 (ppp) REVERT: C 433 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7381 (p90) REVERT: C 552 MET cc_start: 0.7647 (ppp) cc_final: 0.7323 (ppp) REVERT: C 806 LEU cc_start: 0.8096 (pt) cc_final: 0.7674 (pp) REVERT: D 397 GLN cc_start: 0.7970 (mt0) cc_final: 0.7586 (tp40) REVERT: D 482 ARG cc_start: 0.7931 (tmt170) cc_final: 0.7667 (tpt-90) REVERT: D 536 ILE cc_start: 0.8186 (mt) cc_final: 0.7857 (tp) REVERT: D 773 MET cc_start: 0.4418 (mmm) cc_final: 0.4156 (mpp) REVERT: D 810 MET cc_start: 0.8812 (mmt) cc_final: 0.8413 (mtt) REVERT: D 838 SER cc_start: 0.7219 (t) cc_final: 0.6920 (p) REVERT: D 879 MET cc_start: 0.7409 (pmm) cc_final: 0.7063 (pmm) REVERT: E 435 MET cc_start: 0.7849 (mmt) cc_final: 0.7492 (tpt) REVERT: E 441 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5929 (mt-10) REVERT: E 653 MET cc_start: 0.7386 (pmm) cc_final: 0.6484 (pmm) REVERT: E 685 ASP cc_start: 0.8356 (t0) cc_final: 0.7746 (p0) REVERT: E 783 SER cc_start: 0.8953 (t) cc_final: 0.8690 (p) REVERT: F 272 MET cc_start: 0.0933 (ptp) cc_final: 0.0375 (ptp) REVERT: F 435 MET cc_start: 0.8333 (tmm) cc_final: 0.8095 (ttm) REVERT: F 671 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7918 (tm-30) outliers start: 30 outliers final: 27 residues processed: 223 average time/residue: 0.8876 time to fit residues: 332.5972 Evaluate side-chains 227 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 593 ASP Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 637 CYS Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 926 PHE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 211 HIS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 908 THR Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 20.0000 chunk 390 optimal weight: 0.0570 chunk 112 optimal weight: 0.0870 chunk 337 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 367 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 376 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.162128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.122737 restraints weight = 270495.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.122357 restraints weight = 219869.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.123265 restraints weight = 135388.129| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37644 Z= 0.139 Angle : 0.525 7.843 50856 Z= 0.259 Chirality : 0.038 0.153 5832 Planarity : 0.003 0.042 6528 Dihedral : 5.881 111.931 5130 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.54 % Allowed : 12.32 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4632 helix: 1.15 (0.12), residues: 2053 sheet: -2.32 (0.22), residues: 550 loop : -1.29 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 470 HIS 0.005 0.001 HIS A 211 PHE 0.021 0.001 PHE B 421 TYR 0.014 0.001 TYR A 360 ARG 0.003 0.000 ARG E 672 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9735.26 seconds wall clock time: 168 minutes 33.98 seconds (10113.98 seconds total)