Starting phenix.real_space_refine on Sun Sep 29 19:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oka_16923/09_2024/8oka_16923_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oka_16923/09_2024/8oka_16923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oka_16923/09_2024/8oka_16923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oka_16923/09_2024/8oka_16923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oka_16923/09_2024/8oka_16923_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oka_16923/09_2024/8oka_16923_trim.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 23466 2.51 5 N 6432 2.21 5 O 6984 1.98 5 H 37750 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74806 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 12441 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 32, 'TRANS': 744} Chain breaks: 1 Chain: "B" Number of atoms: 12441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 12441 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 32, 'TRANS': 744} Chain breaks: 1 Chain: "C" Number of atoms: 12441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 12441 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 32, 'TRANS': 744} Chain breaks: 1 Chain: "D" Number of atoms: 12441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 12441 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 32, 'TRANS': 744} Chain breaks: 1 Chain: "E" Number of atoms: 12441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 12441 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 32, 'TRANS': 744} Chain breaks: 1 Chain: "F" Number of atoms: 12439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 12439 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 32, 'TRANS': 744} 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: 27.71, per 1000 atoms: 0.37 Number of scatterers: 74806 At special positions: 0 Unit cell: (146.421, 146.421, 224.721, 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 6984 8.00 N 6432 7.00 C 23466 6.00 H 37750 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: 16.73 Conformation dependent library (CDL) restraints added in 4.6 seconds 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8748 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 43 sheets defined 52.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.968A pdb=" N GLU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 288 through 307 removed outlier: 3.890A pdb=" N LEU A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.728A pdb=" N ARG A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.696A 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 403 removed outlier: 3.965A pdb=" N GLY A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 4.353A pdb=" N GLU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.822A pdb=" N ILE A 468 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 511 Processing helix chain 'A' and resid 528 through 540 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.566A pdb=" N GLN A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.744A pdb=" N ALA A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.526A pdb=" N ASP A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 704 removed outlier: 3.635A pdb=" N CYS A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 730 Processing helix chain 'A' and resid 738 through 747 removed outlier: 3.651A pdb=" N ASP A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 852 through 855 Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 924 through 929 removed outlier: 3.707A pdb=" N THR A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.887A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.526A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 removed outlier: 4.232A pdb=" N VAL B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 307 removed outlier: 4.234A pdb=" N ALA B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 327 through 339 removed outlier: 3.861A pdb=" N THR B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 354 through 389 Processing helix chain 'B' and resid 391 through 404 removed outlier: 4.116A pdb=" N LEU B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.920A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 Processing helix chain 'B' and resid 452 through 468 removed outlier: 4.079A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.636A pdb=" N ALA B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 602 through 612 removed outlier: 4.134A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 646 through 653 Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 704 removed outlier: 3.850A pdb=" N CYS B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 730 Processing helix chain 'B' and resid 738 through 747 removed outlier: 3.948A pdb=" N GLN B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 852 through 855 Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 922 Processing helix chain 'B' and resid 924 through 929 removed outlier: 3.578A pdb=" N THR B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 947 removed outlier: 4.091A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 288 through 307 removed outlier: 4.055A pdb=" N LEU C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.642A pdb=" N LEU C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 354 through 389 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.795A pdb=" N LEU C 395 " --> pdb=" O HIS C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.141A pdb=" N LYS C 414 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 427 removed outlier: 3.635A pdb=" N GLU C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.707A pdb=" N ILE C 468 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'C' and resid 528 through 541 Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.695A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 673 through 682 Processing helix chain 'C' and resid 692 through 704 removed outlier: 4.025A pdb=" N CYS C 704 " --> pdb=" O ILE C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 741 through 747 Processing helix chain 'C' and resid 807 through 829 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 Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 938 through 947 removed outlier: 4.181A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 174 through 181 removed outlier: 3.641A pdb=" N VAL D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 307 removed outlier: 4.286A pdb=" N LEU D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 Processing helix chain 'D' and resid 327 through 338 Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.556A pdb=" N LEU D 346 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 407 removed outlier: 3.529A pdb=" N PHE D 394 " --> pdb=" O THR D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 removed outlier: 4.194A pdb=" N GLU D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 452 through 467 Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 511 Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 554 through 560 removed outlier: 4.192A pdb=" N ILE D 558 " --> pdb=" O ASP D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'D' and resid 603 through 612 Processing helix chain 'D' and resid 614 through 619 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.522A pdb=" N MET D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 removed outlier: 3.593A pdb=" N GLN D 677 " --> pdb=" O TYR D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 738 through 746 removed outlier: 4.128A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 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 Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 924 through 929 Processing helix chain 'D' and resid 938 through 947 removed outlier: 4.027A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.564A pdb=" N VAL E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 307 removed outlier: 4.206A pdb=" N LEU E 292 " --> pdb=" O GLU E 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 318 Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.731A pdb=" N ARG E 323 " --> pdb=" O ALA E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 339 Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 354 through 405 removed outlier: 4.000A pdb=" N LYS E 405 " --> pdb=" O LYS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 411 removed outlier: 3.904A pdb=" N GLU E 410 " --> pdb=" O LEU E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 427 removed outlier: 4.011A pdb=" N GLU E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 Processing helix chain 'E' and resid 452 through 468 removed outlier: 3.618A pdb=" N ILE E 468 " --> pdb=" O TRP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 554 through 559 removed outlier: 4.311A pdb=" N ILE E 558 " --> pdb=" O ASP E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 581 Processing helix chain 'E' and resid 592 through 595 Processing helix chain 'E' and resid 602 through 612 removed outlier: 4.233A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 662 through 673 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 738 through 747 removed outlier: 4.017A pdb=" N GLN E 743 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP E 744 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 852 through 855 Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 906 Processing helix chain 'E' and resid 916 through 923 Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 938 through 947 removed outlier: 4.484A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE E 943 " --> pdb=" O TYR E 939 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 157 through 159 No H-bonds generated for 'chain 'F' and resid 157 through 159' Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 182 through 185 Processing helix chain 'F' and resid 289 through 307 removed outlier: 3.843A pdb=" N THR F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 327 through 339 removed outlier: 3.583A pdb=" N LEU F 331 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 339 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 Processing helix chain 'F' and resid 354 through 390 removed outlier: 3.682A pdb=" N THR F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 410 removed outlier: 4.164A pdb=" N LEU F 395 " --> pdb=" O HIS F 391 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 410 " --> pdb=" O GLU F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 427 removed outlier: 3.734A pdb=" N GLU F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 448 Processing helix chain 'F' and resid 452 through 468 Processing helix chain 'F' and resid 479 through 491 Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 528 through 540 Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.632A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 612 removed outlier: 3.847A pdb=" N ALA F 606 " --> pdb=" O ASP F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 673 removed outlier: 4.008A pdb=" N ALA F 668 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 738 through 747 removed outlier: 4.034A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 852 through 855 Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 923 Processing helix chain 'F' and resid 924 through 929 Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.941A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) removed outlier: 3.818A 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 164 removed outlier: 4.647A pdb=" N LEU A 168 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 548 removed outlier: 3.681A pdb=" N LEU A 519 " --> pdb=" O PHE A 635 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 769 removed outlier: 6.402A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 877 through 879 removed outlier: 3.511A pdb=" N ALA A 878 " --> pdb=" O CYS A 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.543A pdb=" N GLU A 882 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AB1, first strand: chain 'B' and resid 163 through 169 removed outlier: 6.734A pdb=" N VAL B 164 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR B 190 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL B 166 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR B 188 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU B 168 " --> pdb=" O TYR B 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.646A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 639 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 689 through 691 removed outlier: 6.838A pdb=" N LYS B 690 " --> pdb=" O VAL B 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 764 through 769 removed outlier: 6.081A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 877 through 879 removed outlier: 7.024A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 882 through 883 removed outlier: 3.756A pdb=" N GLU B 882 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 139 through 142 Processing sheet with id=AB8, first strand: chain 'C' and resid 163 through 167 Processing sheet with id=AB9, first strand: chain 'C' and resid 544 through 545 removed outlier: 6.760A pdb=" N PHE C 545 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 689 through 691 removed outlier: 6.849A pdb=" N LYS C 690 " --> pdb=" O VAL C 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 764 through 770 removed outlier: 6.194A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 877 through 879 Processing sheet with id=AC4, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.723A pdb=" N GLU C 882 " --> pdb=" O LEU C 890 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AC6, first strand: chain 'D' and resid 163 through 169 removed outlier: 3.885A pdb=" N LEU D 168 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N THR D 188 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 544 through 548 removed outlier: 6.764A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP D 590 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE D 547 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 639 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE D 518 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.968A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 764 through 770 removed outlier: 6.300A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 882 through 883 removed outlier: 3.866A pdb=" N GLU D 882 " --> pdb=" O LEU D 890 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 909 through 913 removed outlier: 6.882A pdb=" N ILE D 910 " --> pdb=" O HIS D 934 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL D 936 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU D 912 " --> pdb=" O VAL D 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AD4, first strand: chain 'E' and resid 163 through 167 Processing sheet with id=AD5, first strand: chain 'E' and resid 547 through 548 removed outlier: 6.430A pdb=" N LEU E 519 " --> pdb=" O CYS E 637 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA E 639 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE E 521 " --> pdb=" O ALA E 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 689 through 690 Processing sheet with id=AD7, first strand: chain 'E' and resid 764 through 765 removed outlier: 5.918A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 768 through 769 Processing sheet with id=AD9, first strand: chain 'E' and resid 877 through 878 Processing sheet with id=AE1, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AE2, first strand: chain 'F' and resid 163 through 166 Processing sheet with id=AE3, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.522A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 689 through 690 removed outlier: 3.989A pdb=" N LYS F 690 " --> pdb=" O VAL F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'F' and resid 764 through 769 Processing sheet with id=AE6, first strand: chain 'F' and resid 877 through 879 removed outlier: 7.646A pdb=" N VAL F 936 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU F 912 " --> pdb=" O VAL F 936 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 882 through 883 1802 hydrogen bonds defined for protein. 5208 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: 29.45 Time building geometry restraints manager: 20.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 37708 1.03 - 1.23: 49 1.23 - 1.42: 14966 1.42 - 1.62: 22425 1.62 - 1.82: 282 Bond restraints: 75430 Sorted by residual: bond pdb=" C LYS E 517 " pdb=" N ILE E 518 " ideal model delta sigma weight residual 1.334 1.309 0.025 1.29e-02 6.01e+03 3.80e+00 bond pdb=" N HIS A 123 " pdb=" CA HIS A 123 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N HIS B 123 " pdb=" CA HIS B 123 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N HIS C 123 " pdb=" CA HIS C 123 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N HIS E 123 " pdb=" CA HIS E 123 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 75425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 135462 1.65 - 3.31: 1411 3.31 - 4.96: 182 4.96 - 6.62: 32 6.62 - 8.27: 2 Bond angle restraints: 137089 Sorted by residual: angle pdb=" N VAL C 549 " pdb=" CA VAL C 549 " pdb=" C VAL C 549 " ideal model delta sigma weight residual 113.47 109.16 4.31 1.01e+00 9.80e-01 1.82e+01 angle pdb=" N VAL C 527 " pdb=" CA VAL C 527 " pdb=" C VAL C 527 " ideal model delta sigma weight residual 113.47 109.48 3.99 1.01e+00 9.80e-01 1.56e+01 angle pdb=" N VAL A 527 " pdb=" CA VAL A 527 " pdb=" C VAL A 527 " ideal model delta sigma weight residual 112.96 109.22 3.74 1.00e+00 1.00e+00 1.40e+01 angle pdb=" N VAL F 527 " pdb=" CA VAL F 527 " pdb=" C VAL F 527 " ideal model delta sigma weight residual 113.20 109.75 3.45 9.60e-01 1.09e+00 1.29e+01 angle pdb=" N VAL F 709 " pdb=" CA VAL F 709 " pdb=" C VAL F 709 " ideal model delta sigma weight residual 113.20 109.92 3.28 9.60e-01 1.09e+00 1.17e+01 ... (remaining 137084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.77: 33897 32.77 - 65.53: 1001 65.53 - 98.30: 36 98.30 - 131.07: 5 131.07 - 163.83: 5 Dihedral angle restraints: 34944 sinusoidal: 19686 harmonic: 15258 Sorted by residual: dihedral pdb=" O2A ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PA ADP E1001 " pdb=" PB ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 103.84 -163.83 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 100.97 -160.96 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PB ADP E1001 " pdb=" PA ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 84.73 -144.73 1 2.00e+01 2.50e-03 4.36e+01 ... (remaining 34941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3935 0.030 - 0.061: 1209 0.061 - 0.091: 399 0.091 - 0.122: 255 0.122 - 0.152: 40 Chirality restraints: 5838 Sorted by residual: chirality pdb=" CA ILE F 636 " pdb=" N ILE F 636 " pdb=" C ILE F 636 " pdb=" CB ILE F 636 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA VAL D 658 " pdb=" N VAL D 658 " pdb=" C VAL D 658 " pdb=" CB VAL D 658 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 518 " pdb=" N ILE A 518 " pdb=" C ILE A 518 " pdb=" CB ILE A 518 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 5835 not shown) Planarity restraints: 10992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 602 " -0.029 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO E 603 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 603 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 603 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 761 " -0.026 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO B 762 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 762 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 762 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 760 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B 761 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 761 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 761 " -0.021 5.00e-02 4.00e+02 ... (remaining 10989 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 1167 2.06 - 2.69: 123118 2.69 - 3.33: 222559 3.33 - 3.96: 271380 3.96 - 4.60: 420673 Nonbonded interactions: 1038897 Sorted by model distance: nonbonded pdb=" OE1 GLU D 846 " pdb=" H GLU D 846 " model vdw 1.423 2.450 nonbonded pdb=" H GLY C 798 " pdb=" O VAL C 836 " model vdw 1.474 2.450 nonbonded pdb=" O GLY D 887 " pdb=" H TYR D 939 " model vdw 1.521 2.450 nonbonded pdb=" O GLY C 887 " pdb=" H TYR C 939 " model vdw 1.549 2.450 nonbonded pdb=" H ILE E 889 " pdb=" O GLU E 937 " model vdw 1.552 2.450 ... (remaining 1038892 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 948 or (resid 949 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name H or name H \ A )) or resid 1001)) selection = (chain 'B' and (resid 123 through 948 or (resid 949 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name H or name H \ A )) or resid 1001)) selection = (chain 'C' and (resid 123 through 948 or (resid 949 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name H or name H \ A )) or resid 1001)) selection = (chain 'D' and (resid 123 through 948 or (resid 949 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name H or name H \ A )) or resid 1001)) selection = (chain 'E' and (resid 123 through 948 or (resid 949 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name H or name H \ A )) or resid 1001)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 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: 1.270 Extract box with map and model: 2.430 Check model and map are aligned: 0.460 Set scattering table: 0.560 Process input model: 129.400 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.290 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.003 0.035 37680 Z= 0.166 Angle : 0.575 8.275 50898 Z= 0.313 Chirality : 0.039 0.152 5838 Planarity : 0.003 0.043 6534 Dihedral : 14.332 163.835 14472 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.05 % Allowed : 9.07 % Favored : 90.88 % 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: -0.26 (0.13), residues: 4638 helix: 1.17 (0.11), residues: 2135 sheet: -1.20 (0.23), residues: 545 loop : -1.36 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 470 HIS 0.005 0.001 HIS A 938 PHE 0.014 0.001 PHE C 547 TYR 0.019 0.001 TYR C 703 ARG 0.005 0.000 ARG D 562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 4.547 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: D 197 MET cc_start: 0.5011 (mpp) cc_final: 0.4090 (mmm) outliers start: 2 outliers final: 2 residues processed: 172 average time/residue: 0.9063 time to fit residues: 264.2341 Evaluate side-chains 172 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 4.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain F residue 826 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 9.9990 chunk 350 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 362 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 269 optimal weight: 0.0980 chunk 419 optimal weight: 10.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN D 640 ASN D 741 ASN F 934 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37680 Z= 0.284 Angle : 0.595 9.096 50898 Z= 0.310 Chirality : 0.040 0.151 5838 Planarity : 0.004 0.043 6534 Dihedral : 7.579 162.918 5129 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.42 % Allowed : 9.59 % Favored : 89.99 % 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: -0.40 (0.12), residues: 4638 helix: 1.08 (0.11), residues: 2209 sheet: -1.31 (0.22), residues: 552 loop : -1.57 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 470 HIS 0.006 0.001 HIS B 491 PHE 0.020 0.001 PHE D 820 TYR 0.014 0.001 TYR F 703 ARG 0.006 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 4.585 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: C 206 MET cc_start: -0.0666 (mmm) cc_final: -0.0888 (mmm) REVERT: D 197 MET cc_start: 0.5066 (mpp) cc_final: 0.4172 (mmm) outliers start: 17 outliers final: 10 residues processed: 180 average time/residue: 0.9488 time to fit residues: 293.2849 Evaluate side-chains 172 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 744 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 285 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 420 optimal weight: 6.9990 chunk 454 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 416 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 337 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37680 Z= 0.268 Angle : 0.566 7.250 50898 Z= 0.293 Chirality : 0.039 0.152 5838 Planarity : 0.004 0.045 6534 Dihedral : 7.386 170.430 5126 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.49 % Allowed : 10.55 % Favored : 88.95 % 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: -0.38 (0.12), residues: 4638 helix: 1.12 (0.11), residues: 2218 sheet: -1.38 (0.22), residues: 551 loop : -1.57 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 470 HIS 0.006 0.001 HIS F 195 PHE 0.021 0.001 PHE D 820 TYR 0.014 0.001 TYR F 703 ARG 0.004 0.000 ARG C 562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 653 MET cc_start: 0.8834 (ptt) cc_final: 0.8510 (ptt) REVERT: D 197 MET cc_start: 0.4937 (mpp) cc_final: 0.3988 (mmm) outliers start: 20 outliers final: 12 residues processed: 187 average time/residue: 0.9376 time to fit residues: 297.0418 Evaluate side-chains 178 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 812 GLU Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 704 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 10.0000 chunk 316 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 282 optimal weight: 6.9990 chunk 421 optimal weight: 5.9990 chunk 446 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 399 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37680 Z= 0.350 Angle : 0.605 6.788 50898 Z= 0.317 Chirality : 0.040 0.143 5838 Planarity : 0.004 0.043 6534 Dihedral : 7.332 169.668 5124 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.94 % Allowed : 11.29 % Favored : 87.77 % 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: -0.58 (0.12), residues: 4638 helix: 0.95 (0.11), residues: 2222 sheet: -1.55 (0.21), residues: 561 loop : -1.63 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 470 HIS 0.006 0.001 HIS A 491 PHE 0.024 0.001 PHE D 820 TYR 0.014 0.001 TYR F 703 ARG 0.004 0.000 ARG F 563 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 4.588 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: B 826 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8015 (mtt) REVERT: D 197 MET cc_start: 0.5007 (mpp) cc_final: 0.4143 (mmm) REVERT: F 699 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8901 (mt) outliers start: 38 outliers final: 24 residues processed: 196 average time/residue: 0.8969 time to fit residues: 302.0114 Evaluate side-chains 184 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 944 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain E residue 812 GLU Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 699 LEU Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 744 ASP Chi-restraints excluded: chain F residue 835 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 332 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 381 optimal weight: 7.9990 chunk 308 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 0.8980 chunk 400 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 HIS ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37680 Z= 0.233 Angle : 0.552 7.694 50898 Z= 0.284 Chirality : 0.039 0.167 5838 Planarity : 0.004 0.043 6534 Dihedral : 7.181 166.970 5124 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.96 % Allowed : 11.61 % Favored : 87.43 % 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: -0.32 (0.12), residues: 4638 helix: 1.20 (0.11), residues: 2225 sheet: -1.48 (0.22), residues: 562 loop : -1.55 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 470 HIS 0.005 0.001 HIS B 491 PHE 0.020 0.001 PHE D 820 TYR 0.013 0.001 TYR F 703 ARG 0.003 0.000 ARG F 563 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 4.542 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: B 826 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8029 (mtt) outliers start: 39 outliers final: 24 residues processed: 201 average time/residue: 0.8880 time to fit residues: 304.7019 Evaluate side-chains 192 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 744 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 6.9990 chunk 402 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 262 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 447 optimal weight: 9.9990 chunk 371 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 234 optimal weight: 0.2980 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 HIS B 277 ASN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37680 Z= 0.284 Angle : 0.570 7.618 50898 Z= 0.295 Chirality : 0.039 0.143 5838 Planarity : 0.004 0.043 6534 Dihedral : 7.106 168.763 5124 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.04 % Allowed : 12.11 % Favored : 86.86 % 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: -0.37 (0.12), residues: 4638 helix: 1.16 (0.11), residues: 2225 sheet: -1.54 (0.22), residues: 560 loop : -1.55 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 470 HIS 0.006 0.001 HIS A 491 PHE 0.021 0.001 PHE D 820 TYR 0.013 0.001 TYR F 703 ARG 0.003 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 4.586 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: A 553 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8256 (t) REVERT: B 826 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8065 (mtt) REVERT: D 197 MET cc_start: 0.5059 (mpp) cc_final: 0.4217 (mmm) REVERT: D 766 MET cc_start: 0.8611 (mtt) cc_final: 0.8403 (mtt) REVERT: D 922 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8882 (t0) outliers start: 42 outliers final: 29 residues processed: 201 average time/residue: 0.9018 time to fit residues: 307.4926 Evaluate side-chains 194 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 922 ASP Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain E residue 812 GLU Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 744 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 326 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 376 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 445 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37680 Z= 0.235 Angle : 0.551 8.514 50898 Z= 0.283 Chirality : 0.039 0.157 5838 Planarity : 0.003 0.043 6534 Dihedral : 6.981 177.206 5124 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.84 % Allowed : 12.65 % Favored : 86.51 % 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: -0.21 (0.13), residues: 4638 helix: 1.30 (0.11), residues: 2236 sheet: -1.43 (0.22), residues: 555 loop : -1.51 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 470 HIS 0.009 0.001 HIS A 451 PHE 0.019 0.001 PHE D 820 TYR 0.012 0.001 TYR F 703 ARG 0.003 0.000 ARG F 563 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 4.593 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 553 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8264 (t) REVERT: B 826 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8012 (mtt) REVERT: D 197 MET cc_start: 0.5061 (mpp) cc_final: 0.4228 (mmm) REVERT: D 922 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8888 (t0) outliers start: 34 outliers final: 26 residues processed: 203 average time/residue: 0.9373 time to fit residues: 321.9315 Evaluate side-chains 194 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 597 ARG Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 392 ARG Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 922 ASP Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain E residue 812 GLU Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 744 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 350 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37680 Z= 0.289 Angle : 0.573 6.859 50898 Z= 0.296 Chirality : 0.039 0.140 5838 Planarity : 0.004 0.044 6534 Dihedral : 6.721 148.577 5124 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.13 % Allowed : 12.85 % Favored : 86.02 % 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: -0.30 (0.13), residues: 4638 helix: 1.19 (0.11), residues: 2241 sheet: -1.42 (0.22), residues: 540 loop : -1.55 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 470 HIS 0.007 0.001 HIS A 451 PHE 0.022 0.001 PHE D 820 TYR 0.012 0.001 TYR F 703 ARG 0.004 0.000 ARG B 538 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 4.579 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 553 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8284 (t) REVERT: B 826 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8006 (mtt) REVERT: D 197 MET cc_start: 0.4989 (mpp) cc_final: 0.4165 (mmm) REVERT: D 922 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8890 (t0) outliers start: 46 outliers final: 33 residues processed: 206 average time/residue: 0.9204 time to fit residues: 319.9381 Evaluate side-chains 201 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 597 ARG Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain D residue 392 ARG Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 922 ASP Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain E residue 812 GLU Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 744 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 chunk 389 optimal weight: 3.9990 chunk 414 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 325 optimal weight: 40.0000 chunk 127 optimal weight: 4.9990 chunk 374 optimal weight: 10.0000 chunk 392 optimal weight: 8.9990 chunk 413 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 37680 Z= 0.313 Angle : 0.594 11.896 50898 Z= 0.307 Chirality : 0.039 0.150 5838 Planarity : 0.004 0.042 6534 Dihedral : 6.613 138.400 5124 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.01 % Allowed : 13.31 % Favored : 85.68 % 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: -0.42 (0.12), residues: 4638 helix: 1.08 (0.11), residues: 2233 sheet: -1.49 (0.22), residues: 548 loop : -1.58 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 470 HIS 0.007 0.001 HIS A 451 PHE 0.023 0.001 PHE D 820 TYR 0.014 0.001 TYR F 703 ARG 0.004 0.000 ARG D 755 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 4.554 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: A 553 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8315 (t) REVERT: B 826 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8024 (mtt) REVERT: D 197 MET cc_start: 0.4798 (mpp) cc_final: 0.3959 (tpt) REVERT: D 922 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8872 (t0) outliers start: 41 outliers final: 35 residues processed: 202 average time/residue: 0.9163 time to fit residues: 312.5124 Evaluate side-chains 201 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 597 ARG Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 392 ARG Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 922 ASP Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 777 THR Chi-restraints excluded: chain E residue 812 GLU Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain F residue 415 ASP Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 744 ASP Chi-restraints excluded: chain F residue 835 LEU Chi-restraints excluded: chain F residue 915 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 0.7980 chunk 438 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 chunk 460 optimal weight: 10.0000 chunk 423 optimal weight: 9.9990 chunk 366 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 283 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37680 Z= 0.167 Angle : 0.546 9.394 50898 Z= 0.274 Chirality : 0.039 0.152 5838 Planarity : 0.003 0.038 6534 Dihedral : 6.360 142.648 5124 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.76 % Allowed : 13.54 % Favored : 85.70 % 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: -0.05 (0.13), residues: 4638 helix: 1.45 (0.11), residues: 2233 sheet: -1.32 (0.22), residues: 534 loop : -1.48 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 470 HIS 0.006 0.001 HIS A 451 PHE 0.014 0.001 PHE B 455 TYR 0.014 0.001 TYR F 703 ARG 0.006 0.000 ARG E 562 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 4.621 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 553 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8295 (t) REVERT: B 826 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8006 (mtt) REVERT: D 197 MET cc_start: 0.4932 (mpp) cc_final: 0.4076 (tpt) REVERT: D 922 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8901 (t0) outliers start: 31 outliers final: 26 residues processed: 201 average time/residue: 0.9403 time to fit residues: 316.6336 Evaluate side-chains 193 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 4.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 597 ARG Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 741 ASN Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 392 ARG Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 922 ASP Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 812 GLU Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 637 CYS Chi-restraints excluded: chain F residue 675 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 6.9990 chunk 390 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 337 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 367 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 376 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.097681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.064502 restraints weight = 498901.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.066379 restraints weight = 208078.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.066406 restraints weight = 107349.022| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37680 Z= 0.180 Angle : 0.543 9.694 50898 Z= 0.272 Chirality : 0.039 0.148 5838 Planarity : 0.003 0.037 6534 Dihedral : 6.187 141.871 5124 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.69 % Allowed : 13.63 % Favored : 85.68 % 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: 0.03 (0.13), residues: 4638 helix: 1.52 (0.11), residues: 2241 sheet: -1.30 (0.22), residues: 538 loop : -1.44 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 470 HIS 0.005 0.001 HIS A 451 PHE 0.016 0.001 PHE D 820 TYR 0.014 0.001 TYR F 703 ARG 0.003 0.000 ARG A 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9122.56 seconds wall clock time: 158 minutes 45.18 seconds (9525.18 seconds total)