Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 12:13:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whx_21679/04_2023/6whx_21679_updated.pdb" } resolution = 4.09 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.019 sd= 1.031 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 2 5.49 5 S 127 5.16 5 Cl 4 4.86 5 C 14733 2.51 5 N 3768 2.21 5 O 4291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C ASP 810": "OD1" <-> "OD2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22925 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5691 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 32, 'TRANS': 758} Chain breaks: 4 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 15, 'TYR:plan': 3, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 379 Chain: "B" Number of atoms: 5729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5729 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 588 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 13, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 314 Chain: "C" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5783 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 32, 'TRANS': 762} Chain breaks: 4 Unresolved non-hydrogen bonds: 516 Unresolved non-hydrogen angles: 625 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 358 Chain: "D" Number of atoms: 5642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5642 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 489 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 18, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 30, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 411 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 11.57, per 1000 atoms: 0.50 Number of scatterers: 22925 At special positions: 0 Unit cell: (134.26, 149.33, 190.43, 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) Cl 4 17.00 S 127 16.00 P 2 15.00 O 4291 8.00 N 3768 7.00 C 14733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.02 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.04 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 159 " " NAG C1001 " - " ASN C 389 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 3.4 seconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 16 sheets defined 33.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.666A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.535A pdb=" N VAL A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.940A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 154 through 157 No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.605A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 5.169A pdb=" N GLU A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.116A pdb=" N LEU A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 4.035A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 removed outlier: 5.493A pdb=" N SER A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.959A pdb=" N THR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 542 through 547 removed outlier: 3.548A pdb=" N GLN A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 547' Processing helix chain 'A' and resid 581 through 603 removed outlier: 4.049A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 removed outlier: 3.823A pdb=" N PHE A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 677 removed outlier: 3.788A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 No H-bonds generated for 'chain 'A' and resid 691 through 694' Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 735 through 744 removed outlier: 4.242A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 800 removed outlier: 3.597A pdb=" N GLN A 791 " --> pdb=" O PRO A 788 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A 793 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 797 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 798 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 812 removed outlier: 3.974A pdb=" N LYS A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 835 through 855 removed outlier: 4.115A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 860 No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'B' and resid 78 through 88 removed outlier: 4.297A pdb=" N ARG B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.707A pdb=" N PHE B 114 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 163 removed outlier: 4.139A pdb=" N MET B 157 " --> pdb=" O GLN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 190 removed outlier: 4.022A pdb=" N THR B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 216 through 219 No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 234 through 247 Processing helix chain 'B' and resid 260 through 263 No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'B' and resid 289 through 309 removed outlier: 4.095A pdb=" N MET B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 4.118A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.691A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 558 through 578 removed outlier: 4.366A pdb=" N VAL B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 4.931A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 651 removed outlier: 3.660A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 676 through 678 No H-bonds generated for 'chain 'B' and resid 676 through 678' Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.505A pdb=" N ASN B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 717 through 721 Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.494A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 739 " --> pdb=" O VAL B 735 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 786 removed outlier: 4.460A pdb=" N GLN B 782 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 795 Processing helix chain 'B' and resid 815 through 843 removed outlier: 4.626A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 38 No H-bonds generated for 'chain 'C' and resid 36 through 38' Processing helix chain 'C' and resid 41 through 50 removed outlier: 4.376A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.732A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 126 through 129 Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.835A pdb=" N SER C 149 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 150 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET C 155 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.701A pdb=" N ALA C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.539A pdb=" N THR C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 302 through 316 removed outlier: 4.003A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 348 removed outlier: 3.930A pdb=" N LEU C 346 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 4.025A pdb=" N ARG C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 527 removed outlier: 3.614A pdb=" N LEU C 526 " --> pdb=" O MET C 522 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 527 " --> pdb=" O MET C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 583 through 602 Processing helix chain 'C' and resid 625 through 633 removed outlier: 4.930A pdb=" N PHE C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 673 removed outlier: 4.396A pdb=" N ILE C 652 " --> pdb=" O PHE C 648 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 659 " --> pdb=" O MET C 655 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 694 No H-bonds generated for 'chain 'C' and resid 691 through 694' Processing helix chain 'C' and resid 710 through 715 Processing helix chain 'C' and resid 718 through 729 removed outlier: 4.034A pdb=" N THR C 722 " --> pdb=" O GLU C 719 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG C 725 " --> pdb=" O THR C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 742 removed outlier: 4.961A pdb=" N VAL C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 762 removed outlier: 4.682A pdb=" N SER C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 801 removed outlier: 4.257A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C 800 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS C 801 " --> pdb=" O ILE C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 835 through 849 removed outlier: 3.653A pdb=" N GLY C 848 " --> pdb=" O GLY C 844 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 857 No H-bonds generated for 'chain 'C' and resid 854 through 857' Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.533A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 removed outlier: 4.466A pdb=" N MET D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 187 removed outlier: 5.232A pdb=" N ASN D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 217 through 220 No H-bonds generated for 'chain 'D' and resid 217 through 220' Processing helix chain 'D' and resid 234 through 246 removed outlier: 4.055A pdb=" N SER D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 310 removed outlier: 3.640A pdb=" N MET D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 444 through 446 No H-bonds generated for 'chain 'D' and resid 444 through 446' Processing helix chain 'D' and resid 461 through 472 removed outlier: 3.633A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 502 removed outlier: 5.026A pdb=" N VAL D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 577 removed outlier: 4.044A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET D 561 " --> pdb=" O CYS D 557 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 611 removed outlier: 3.755A pdb=" N TRP D 610 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 651 removed outlier: 5.473A pdb=" N VAL D 632 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 643 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR D 647 " --> pdb=" O ALA D 644 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU D 650 " --> pdb=" O THR D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 692 through 697 removed outlier: 3.880A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 706 removed outlier: 3.865A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 716 No H-bonds generated for 'chain 'D' and resid 714 through 716' Processing helix chain 'D' and resid 734 through 742 removed outlier: 4.361A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG D 742 " --> pdb=" O TYR D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 785 removed outlier: 3.916A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 796 Processing helix chain 'D' and resid 815 through 843 removed outlier: 5.537A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 823 " --> pdb=" O ALA D 819 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N MET D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU D 841 " --> pdb=" O ILE D 837 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= B, first strand: chain 'A' and resid 290 through 292 removed outlier: 4.110A pdb=" N GLN A 291 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 374 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY A 386 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 559 through 562 removed outlier: 3.800A pdb=" N THR A 560 " --> pdb=" O TRP A 752 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 171 through 173 Processing sheet with id= E, first strand: chain 'B' and resid 227 through 229 removed outlier: 5.967A pdb=" N THR B 255 " --> pdb=" O ILE B 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.233A pdb=" N THR B 475 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE B 408 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASP B 477 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR B 410 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR B 479 " --> pdb=" O THR B 410 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.667A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 508 through 510 Processing sheet with id= I, first strand: chain 'B' and resid 537 through 539 removed outlier: 3.761A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 364 through 367 removed outlier: 6.241A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 290 through 292 removed outlier: 3.513A pdb=" N GLN C 291 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 376 " --> pdb=" O VAL C 383 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 455 through 459 removed outlier: 3.530A pdb=" N VAL C 455 " --> pdb=" O CYS C 476 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 97 through 99 removed outlier: 3.593A pdb=" N LEU D 124 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY D 125 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 278 through 281 removed outlier: 3.870A pdb=" N ILE D 365 " --> pdb=" O SER D 279 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER D 281 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 408 through 410 removed outlier: 4.071A pdb=" N THR D 410 " --> pdb=" O TYR D 479 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.562A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1431 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: 6.74 Time building geometry restraints manager: 10.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7372 1.34 - 1.46: 5627 1.46 - 1.58: 10190 1.58 - 1.70: 2 1.70 - 1.82: 216 Bond restraints: 23407 Sorted by residual: bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.862 1.661 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.862 1.662 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C4 QGP D 901 " pdb=" O6 QGP D 901 " ideal model delta sigma weight residual 1.401 1.227 0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C4 QGP B 901 " pdb=" O6 QGP B 901 " ideal model delta sigma weight residual 1.401 1.230 0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C12 QGP B 901 " pdb=" C7 QGP B 901 " ideal model delta sigma weight residual 1.527 1.369 0.158 2.00e-02 2.50e+03 6.21e+01 ... (remaining 23402 not shown) Histogram of bond angle deviations from ideal: 97.57 - 106.44: 622 106.44 - 115.31: 14502 115.31 - 124.18: 16398 124.18 - 133.05: 416 133.05 - 141.92: 55 Bond angle restraints: 31993 Sorted by residual: angle pdb=" C VAL D 422 " pdb=" N ASP D 423 " pdb=" CA ASP D 423 " ideal model delta sigma weight residual 122.48 140.93 -18.45 1.77e+00 3.19e-01 1.09e+02 angle pdb=" N VAL D 776 " pdb=" CA VAL D 776 " pdb=" C VAL D 776 " ideal model delta sigma weight residual 113.53 105.41 8.12 9.80e-01 1.04e+00 6.87e+01 angle pdb=" N VAL B 735 " pdb=" CA VAL B 735 " pdb=" C VAL B 735 " ideal model delta sigma weight residual 113.43 107.19 6.24 1.09e+00 8.42e-01 3.27e+01 angle pdb=" N VAL C 742 " pdb=" CA VAL C 742 " pdb=" C VAL C 742 " ideal model delta sigma weight residual 113.42 107.35 6.07 1.17e+00 7.31e-01 2.69e+01 angle pdb=" N ILE A 275 " pdb=" CA ILE A 275 " pdb=" C ILE A 275 " ideal model delta sigma weight residual 111.91 107.32 4.59 8.90e-01 1.26e+00 2.66e+01 ... (remaining 31988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12291 17.87 - 35.73: 1191 35.73 - 53.60: 195 53.60 - 71.47: 26 71.47 - 89.33: 18 Dihedral angle restraints: 13721 sinusoidal: 4599 harmonic: 9122 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 329 " pdb=" CB CYS C 329 " ideal model delta sinusoidal sigma weight residual -86.00 -3.02 -82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CA ILE A 322 " pdb=" C ILE A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta harmonic sigma weight residual -180.00 -140.02 -39.98 0 5.00e+00 4.00e-02 6.39e+01 dihedral pdb=" CB CYS B 557 " pdb=" SG CYS B 557 " pdb=" SG CYS C 831 " pdb=" CB CYS C 831 " ideal model delta sinusoidal sigma weight residual 93.00 155.87 -62.87 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 13718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2869 0.054 - 0.108: 828 0.108 - 0.161: 124 0.161 - 0.215: 10 0.215 - 0.269: 1 Chirality restraints: 3832 Sorted by residual: chirality pdb=" CB ILE A 287 " pdb=" CA ILE A 287 " pdb=" CG1 ILE A 287 " pdb=" CG2 ILE A 287 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA VAL C 141 " pdb=" N VAL C 141 " pdb=" C VAL C 141 " pdb=" CB VAL C 141 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 3829 not shown) Planarity restraints: 4058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 105 " -0.060 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO C 106 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 679 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.94e+00 pdb=" N PRO B 680 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 680 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 680 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 787 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.41e+00 pdb=" N PRO C 788 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 788 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 788 " 0.037 5.00e-02 4.00e+02 ... (remaining 4055 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 443 2.62 - 3.19: 22788 3.19 - 3.76: 32632 3.76 - 4.33: 43210 4.33 - 4.90: 65795 Nonbonded interactions: 164868 Sorted by model distance: nonbonded pdb=" O ILE B 115 " pdb=" OG1 THR B 119 " model vdw 2.048 2.440 nonbonded pdb=" OG SER D 131 " pdb=" O PHE D 146 " model vdw 2.102 2.440 nonbonded pdb=" OG1 THR D 343 " pdb=" O ARG D 347 " model vdw 2.103 2.440 nonbonded pdb=" OH TYR B 167 " pdb=" OG1 THR B 428 " model vdw 2.112 2.440 nonbonded pdb=" O GLY C 328 " pdb=" ND2 ASN C 332 " model vdw 2.118 2.520 ... (remaining 164863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 36 or (resid 37 through 45 and (na \ me N or name CA or name C or name O or name CB )) or resid 46 through 47 or (res \ id 48 through 49 and (name N or name CA or name C or name O or name CB )) or res \ id 50 through 58 or (resid 59 and (name N or name CA or name C or name O or name \ CB )) or resid 60 or (resid 61 through 62 and (name N or name CA or name C or n \ ame O or name CB )) or resid 63 through 66 or (resid 67 and (name N or name CA o \ r name C or name O or name CB )) or resid 68 through 79 or (resid 80 through 81 \ and (name N or name CA or name C or name O or name CB )) or resid 82 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 8 through 114 or (resid 115 and (name N or name CA or name C or name O or name C \ B )) or resid 116 through 145 or (resid 146 and (name N or name CA or name C or \ name O or name CB )) or resid 147 through 158 or (resid 159 and (name N or name \ CA or name C or name O or name CB )) or resid 160 through 161 or (resid 162 and \ (name N or name CA or name C or name O or name CB )) or resid 163 through 168 or \ (resid 169 through 170 and (name N or name CA or name C or name O or name CB )) \ or resid 171 through 178 or (resid 179 and (name N or name CA or name C or name \ O or name CB )) or resid 180 through 230 or (resid 231 through 232 and (name N \ or name CA or name C or name O or name CB )) or resid 233 or (resid 234 and (nam \ e N or name CA or name C or name O or name CB )) or resid 235 through 265 or (re \ sid 266 and (name N or name CA or name C or name O or name CB )) or resid 267 th \ rough 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) \ or resid 276 through 277 or (resid 278 through 283 and (name N or name CA or na \ me C or name O or name CB )) or resid 284 through 291 or (resid 292 through 293 \ and (name N or name CA or name C or name O or name CB )) or resid 294 through 31 \ 3 or (resid 314 through 315 and (name N or name CA or name C or name O or name C \ B )) or resid 316 through 329 or (resid 330 and (name N or name CA or name C or \ name O or name CB )) or resid 331 through 333 or (resid 334 and (name N or name \ CA or name C or name O or name CB )) or resid 335 through 342 or (resid 343 thro \ ugh 344 and (name N or name CA or name C or name O or name CB )) or resid 345 th \ rough 395 or (resid 396 through 399 and (name N or name CA or name C or name O o \ r name CB )) or resid 400 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 432 or (resid 433 and (name N \ or name CA or name C or name O or name CB )) or resid 434 through 509 or (resid \ 510 and (name N or name CA or name C or name O or name CB )) or resid 511 throug \ h 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 542 or (resid 543 and (name N or name CA or name C or name O o \ r name CB )) or resid 544 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 583 or (resid 584 and (name N \ or name CA or name C or name O or name CB )) or resid 585 through 681 or (resid \ 682 through 684 and (name N or name CA or name C or name O or name CB )) or resi \ d 685 through 724 or (resid 725 and (name N or name CA or name C or name O or na \ me CB )) or resid 726 through 789 or (resid 790 and (name N or name CA or name C \ or name O or name CB )) or resid 791 through 821 or (resid 822 and (name N or n \ ame CA or name C or name O or name CB )) or resid 823 through 862 or resid 1001) \ ) selection = (chain 'C' and (resid 25 through 38 or (resid 39 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 through 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 72 or (res \ id 73 through 75 and (name N or name CA or name C or name O or name CB )) or res \ id 76 through 108 or (resid 109 and (name N or name CA or name C or name O or na \ me CB )) or resid 110 through 129 or (resid 130 through 131 and (name N or name \ CA or name C or name O or name CB )) or resid 132 through 136 or (resid 137 and \ (name N or name CA or name C or name O or name CB )) or resid 138 or (resid 139 \ and (name N or name CA or name C or name O or name CB )) or resid 140 through 15 \ 5 or (resid 156 and (name N or name CA or name C or name O or name CB )) or resi \ d 157 through 180 or (resid 181 and (name N or name CA or name C or name O or na \ me CB )) or resid 182 through 184 or (resid 185 and (name N or name CA or name C \ or name O or name CB )) or resid 186 through 190 or resid 208 through 210 or (r \ esid 211 through 212 and (name N or name CA or name C or name O or name CB )) or \ resid 213 through 221 or (resid 222 through 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225 through 253 or (resid 254 through 262 and \ (name N or name CA or name C or name O or name CB )) or resid 263 through 284 o \ r (resid 285 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 86 through 292 or (resid 293 and (name N or name CA or name C or name O or name \ CB )) or resid 294 through 303 or (resid 304 through 305 and (name N or name CA \ or name C or name O or name CB )) or resid 306 through 310 or (resid 311 through \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throu \ gh 323 or (resid 324 and (name N or name CA or name C or name O or name CB )) or \ resid 325 through 336 or (resid 337 and (name N or name CA or name C or name O \ or name CB )) or resid 338 through 357 or (resid 358 and (name N or name CA or n \ ame C or name O or name CB )) or resid 359 or (resid 360 and (name N or name CA \ or name C or name O or name CB )) or resid 361 through 367 or (resid 368 and (na \ me N or name CA or name C or name O or name CB )) or resid 369 through 374 or (r \ esid 375 and (name N or name CA or name C or name O or name CB )) or resid 376 t \ hrough 377 or (resid 378 through 381 and (name N or name CA or name C or name O \ or name CB )) or resid 382 through 390 or (resid 391 through 392 and (name N or \ name CA or name C or name O or name CB )) or resid 393 through 410 or (resid 411 \ and (name N or name CA or name C or name O or name CB )) or resid 412 through 4 \ 14 or (resid 415 and (name N or name CA or name C or name O or name CB )) or res \ id 416 through 417 or (resid 418 and (name N or name CA or name C or name O or n \ ame CB )) or resid 419 through 435 or (resid 436 and (name N or name CA or name \ C or name O or name CB )) or resid 437 through 443 or (resid 444 and (name N or \ name CA or name C or name O or name CB )) or resid 445 through 447 or (resid 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 451 throu \ gh 452 or (resid 453 and (name N or name CA or name C or name O or name CB )) or \ resid 454 through 461 or (resid 462 through 463 and (name N or name CA or name \ C or name O or name CB )) or resid 464 through 486 or (resid 487 through 488 and \ (name N or name CA or name C or name O or name CB )) or resid 489 through 490 o \ r (resid 491 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 92 through 503 or (resid 504 and (name N or name CA or name C or name O or name \ CB )) or resid 505 through 507 or (resid 508 through 510 and (name N or name CA \ or name C or name O or name CB )) or resid 511 through 548 or (resid 549 and (na \ me N or name CA or name C or name O or name CB )) or resid 550 through 565 or (r \ esid 566 and (name N or name CA or name C or name O or name CB )) or resid 567 t \ hrough 568 or (resid 569 and (name N or name CA or name C or name O or name CB ) \ ) or resid 570 through 571 or (resid 572 and (name N or name CA or name C or nam \ e O or name CB )) or resid 573 through 641 or (resid 642 and (name N or name CA \ or name C or name O or name CB )) or resid 643 through 691 or (resid 692 and (na \ me N or name CA or name C or name O or name CB )) or resid 693 through 698 or (r \ esid 699 and (name N or name CA or name C or name O or name CB )) or resid 700 t \ hrough 714 or (resid 715 through 716 and (name N or name CA or name C or name O \ or name CB )) or resid 717 through 723 or (resid 724 through 725 and (name N or \ name CA or name C or name O or name CB )) or resid 726 through 728 or (resid 729 \ and (name N or name CA or name C or name O or name CB )) or resid 730 through 7 \ 42 or (resid 743 and (name N or name CA or name C or name O or name CB )) or res \ id 744 through 784 or (resid 785 and (name N or name CA or name C or name O or n \ ame CB )) or resid 786 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 816 or (resid 817 through 818 and \ (name N or name CA or name C or name O or name CB )) or resid 819 through 862 o \ r resid 1001)) } ncs_group { reference = (chain 'B' and (resid 34 or (resid 35 and (name N or name CA or name C or name O \ or name CB )) or resid 36 through 43 or (resid 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 through 58 or (resid 59 through 62 and ( \ name N or name CA or name C or name O or name CB )) or resid 63 through 66 or (r \ esid 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or \ (resid 69 and (name N or name CA or name C or name O or name CB )) or resid 70 t \ hrough 72 or (resid 73 through 75 and (name N or name CA or name C or name O or \ name CB )) or resid 76 or (resid 77 and (name N or name CA or name C or name O o \ r name CB )) or resid 78 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 94 or (resid 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 101 or (resid 102 and \ (name N or name CA or name C or name O or name CB )) or resid 103 or (resid 104 \ through 107 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 08 through 109 or (resid 110 and (name N or name CA or name C or name O or name \ CB )) or resid 111 through 112 or (resid 113 and (name N or name CA or name C or \ name O or name CB )) or resid 114 through 119 or (resid 120 and (name N or name \ CA or name C or name O or name CB )) or resid 121 through 137 or (resid 138 thr \ ough 139 and (name N or name CA or name C or name O or name CB )) or resid 140 t \ hrough 200 or (resid 201 and (name N or name CA or name C or name O or name CB ) \ ) or resid 202 through 221 or (resid 222 and (name N or name CA or name C or nam \ e O or name CB )) or resid 223 through 234 or (resid 235 through 237 and (name N \ or name CA or name C or name O or name CB )) or resid 238 through 241 or (resid \ 242 and (name N or name CA or name C or name O or name CB )) or resid 243 throu \ gh 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 271 or (resid 272 and (name N or name CA or name C or name O \ or name CB )) or resid 273 through 283 or (resid 284 and (name N or name CA or n \ ame C or name O or name CB )) or resid 285 through 286 or (resid 287 and (name N \ or name CA or name C or name O or name CB )) or resid 288 through 325 or (resid \ 326 through 331 and (name N or name CA or name C or name O or name CB )) or res \ id 332 through 381 or (resid 382 and (name N or name CA or name C or name O or n \ ame CB )) or resid 383 through 394 or (resid 403 and (name N or name CA or name \ C or name O or name CB )) or resid 404 through 411 or (resid 412 through 414 and \ (name N or name CA or name C or name O or name CB )) or resid 415 through 419 o \ r (resid 420 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 21 through 422 or (resid 423 and (name N or name CA or name C or name O or name \ CB )) or resid 424 or (resid 425 and (name N or name CA or name C or name O or n \ ame CB )) or resid 426 through 445 or (resid 446 through 449 and (name N or name \ CA or name C or name O or name CB )) or resid 450 through 451 or (resid 452 and \ (name N or name CA or name C or name O or name CB )) or resid 453 through 454 o \ r (resid 455 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 56 through 472 or (resid 473 and (name N or name CA or name C or name O or name \ CB )) or resid 474 through 516 or (resid 517 and (name N or name CA or name C or \ name O or name CB )) or resid 518 through 539 or (resid 540 and (name N or name \ CA or name C or name O or name CB )) or resid 541 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 552 \ and (name N or name CA or name C or name O or name CB )) or resid 553 through 5 \ 62 or (resid 563 and (name N or name CA or name C or name O or name CB )) or res \ id 564 through 621 or (resid 622 and (name N or name CA or name C or name O or n \ ame CB )) or resid 623 through 656 or (resid 657 and (name N or name CA or name \ C or name O or name CB )) or resid 658 through 669 or (resid 670 through 671 and \ (name N or name CA or name C or name O or name CB )) or resid 672 or (resid 673 \ and (name N or name CA or name C or name O or name CB )) or resid 674 through 7 \ 10 or (resid 711 through 712 and (name N or name CA or name C or name O or name \ CB )) or resid 713 through 715 or (resid 716 through 717 and (name N or name CA \ or name C or name O or name CB )) or resid 718 or (resid 719 and (name N or name \ CA or name C or name O or name CB )) or resid 720 through 726 or (resid 727 thr \ ough 728 and (name N or name CA or name C or name O or name CB )) or resid 729 t \ hrough 741 or (resid 742 through 744 and (name N or name CA or name C or name O \ or name CB )) or resid 745 through 746 or (resid 747 and (name N or name CA or n \ ame C or name O or name CB )) or resid 748 through 801 or (resid 802 and (name N \ or name CA or name C or name O or name CB )) or resid 803 through 805 or (resid \ 806 through 807 and (name N or name CA or name C or name O or name CB )) or res \ id 808 through 816 or (resid 817 through 819 and (name N or name CA or name C or \ name O or name CB )) or resid 820 through 822 or (resid 823 and (name N or name \ CA or name C or name O or name CB )) or resid 824 through 838 or (resid 839 and \ (name N or name CA or name C or name O or name CB )) or resid 840 through 845 o \ r resid 901)) selection = (chain 'D' and (resid 34 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 51 or (resid 52 through 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 90 or (resid 91 through 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 117 or (resid 118 and (name N or name CA or name C or \ name O or name CB )) or resid 119 through 126 or (resid 127 and (name N or name \ CA or name C or name O or name CB )) or resid 128 through 144 or (resid 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 through 199 o \ r (resid 200 through 201 and (name N or name CA or name C or name O or name CB ) \ ) or resid 202 through 205 or (resid 206 through 207 and (name N or name CA or n \ ame C or name O or name CB )) or resid 208 through 209 or (resid 210 through 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 18 or (resid 219 and (name N or name CA or name C or name O or name CB )) or res \ id 220 through 281 or (resid 282 through 284 and (name N or name CA or name C or \ name O or name CB )) or resid 285 through 309 or (resid 310 and (name N or name \ CA or name C or name O or name CB )) or resid 311 through 313 or (resid 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 321 o \ r (resid 322 through 331 and (name N or name CA or name C or name O or name CB ) \ ) or resid 332 or (resid 333 and (name N or name CA or name C or name O or name \ CB )) or resid 334 through 336 or (resid 337 and (name N or name CA or name C or \ name O or name CB )) or resid 338 through 343 or (resid 344 through 345 and (na \ me N or name CA or name C or name O or name CB )) or resid 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 or (resid 349 \ and (name N or name CA or name C or name O or name CB )) or resid 350 through 3 \ 68 or (resid 369 through 370 and (name N or name CA or name C or name O or name \ CB )) or resid 371 through 377 or (resid 378 and (name N or name CA or name C or \ name O or name CB )) or resid 379 through 386 or (resid 387 and (name N or name \ CA or name C or name O or name CB )) or resid 388 through 484 or (resid 485 and \ (name N or name CA or name C or name O or name CB )) or resid 486 through 487 o \ r (resid 488 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 89 through 623 or (resid 624 and (name N or name CA or name C or name O or name \ CB )) or resid 625 through 628 or (resid 629 and (name N or name CA or name C or \ name O or name CB )) or resid 630 through 668 or (resid 669 through 671 and (na \ me N or name CA or name C or name O or name CB )) or resid 672 through 691 or (r \ esid 692 and (name N or name CA or name C or name O or name CB )) or resid 693 t \ hrough 698 or (resid 699 through 700 and (name N or name CA or name C or name O \ or name CB )) or resid 701 through 804 or (resid 805 through 807 and (name N or \ name CA or name C or name O or name CB )) or resid 808 through 835 or (resid 836 \ and (name N or name CA or name C or name O or name CB )) or resid 837 through 8 \ 41 or (resid 842 through 845 and (name N or name CA or name C or name O or name \ CB )) or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.890 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 55.230 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.007 0.201 23407 Z= 0.466 Angle : 0.866 20.514 31993 Z= 0.488 Chirality : 0.049 0.269 3832 Planarity : 0.006 0.091 4056 Dihedral : 14.575 89.334 7785 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 19.41 % Favored : 80.56 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.03 % 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: -5.50 (0.12), residues: 3122 helix: -3.16 (0.12), residues: 990 sheet: -4.03 (0.23), residues: 299 loop : -4.06 (0.12), residues: 1833 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 382 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 384 average time/residue: 0.3183 time to fit residues: 196.8748 Evaluate side-chains 281 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1955 time to fit residues: 4.2993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 0.9980 chunk 237 optimal weight: 9.9990 chunk 132 optimal weight: 0.0030 chunk 81 optimal weight: 0.3980 chunk 160 optimal weight: 30.0000 chunk 127 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 426 GLN A 498 HIS A 530 GLN A 542 ASN A 726 HIS ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS B 180 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 294 ASN C 542 ASN C 671 ASN C 717 GLN C 730 HIS D 224 GLN D 359 HIS D 495 ASN ** D 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 23407 Z= 0.185 Angle : 0.641 15.367 31993 Z= 0.331 Chirality : 0.045 0.273 3832 Planarity : 0.005 0.083 4056 Dihedral : 6.461 54.201 3305 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.93 % Favored : 90.04 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.03 % 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: -4.16 (0.13), residues: 3122 helix: -1.81 (0.15), residues: 997 sheet: -3.29 (0.26), residues: 294 loop : -3.39 (0.13), residues: 1831 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 408 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 410 average time/residue: 0.2796 time to fit residues: 193.2280 Evaluate side-chains 296 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 295 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2017 time to fit residues: 4.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 0.0020 chunk 88 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 308 optimal weight: 7.9990 chunk 254 optimal weight: 0.0000 chunk 283 optimal weight: 0.0870 chunk 97 optimal weight: 20.0000 chunk 229 optimal weight: 0.4980 overall best weight: 1.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 542 ASN ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 23407 Z= 0.165 Angle : 0.599 13.342 31993 Z= 0.307 Chirality : 0.044 0.242 3832 Planarity : 0.005 0.083 4056 Dihedral : 5.751 55.559 3305 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.25 % Favored : 89.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -3.40 (0.14), residues: 3122 helix: -1.07 (0.17), residues: 1001 sheet: -2.94 (0.27), residues: 291 loop : -2.97 (0.14), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.2914 time to fit residues: 202.0661 Evaluate side-chains 314 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 191 optimal weight: 20.0000 chunk 286 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 271 optimal weight: 0.1980 chunk 81 optimal weight: 40.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A 801 HIS B 311 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 23407 Z= 0.242 Angle : 0.633 13.908 31993 Z= 0.323 Chirality : 0.045 0.234 3832 Planarity : 0.005 0.083 4056 Dihedral : 5.887 53.691 3305 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.88 % Favored : 88.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -3.23 (0.14), residues: 3122 helix: -0.98 (0.16), residues: 1023 sheet: -2.97 (0.27), residues: 298 loop : -2.83 (0.14), residues: 1801 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2993 time to fit residues: 194.1783 Evaluate side-chains 297 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 259 optimal weight: 0.0570 chunk 209 optimal weight: 0.2980 chunk 0 optimal weight: 40.0000 chunk 154 optimal weight: 9.9990 chunk 272 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 overall best weight: 1.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS A 833 ASN B 311 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23407 Z= 0.171 Angle : 0.590 12.827 31993 Z= 0.299 Chirality : 0.044 0.228 3832 Planarity : 0.004 0.081 4056 Dihedral : 5.423 53.527 3305 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.32 % Favored : 90.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.15), residues: 3122 helix: -0.73 (0.17), residues: 1020 sheet: -2.73 (0.27), residues: 319 loop : -2.57 (0.14), residues: 1783 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.2921 time to fit residues: 192.4317 Evaluate side-chains 313 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 303 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 140 optimal weight: 0.0010 chunk 25 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS A 833 ASN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS C 470 HIS C 542 ASN D 385 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 23407 Z= 0.153 Angle : 0.581 12.205 31993 Z= 0.291 Chirality : 0.043 0.251 3832 Planarity : 0.004 0.080 4056 Dihedral : 5.066 55.635 3305 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.14 % Favored : 91.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.15), residues: 3122 helix: -0.53 (0.17), residues: 1015 sheet: -2.58 (0.27), residues: 316 loop : -2.37 (0.14), residues: 1791 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.899 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 outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.2910 time to fit residues: 199.1920 Evaluate side-chains 320 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 255 optimal weight: 0.0060 chunk 169 optimal weight: 4.9990 chunk 302 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23407 Z= 0.218 Angle : 0.613 13.755 31993 Z= 0.310 Chirality : 0.045 0.287 3832 Planarity : 0.005 0.079 4056 Dihedral : 5.307 55.563 3305 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.31 % Favored : 89.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.15), residues: 3122 helix: -0.43 (0.17), residues: 1003 sheet: -2.45 (0.27), residues: 321 loop : -2.32 (0.15), residues: 1798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.3022 time to fit residues: 196.2262 Evaluate side-chains 302 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.497 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 180 optimal weight: 0.0030 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 192 optimal weight: 0.0980 chunk 206 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 28 optimal weight: 0.0370 chunk 237 optimal weight: 6.9990 overall best weight: 0.6270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS C 384 GLN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 23407 Z= 0.146 Angle : 0.573 12.389 31993 Z= 0.287 Chirality : 0.043 0.267 3832 Planarity : 0.004 0.078 4056 Dihedral : 4.865 55.607 3305 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.66 % Favored : 92.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 3122 helix: -0.28 (0.17), residues: 1010 sheet: -2.51 (0.27), residues: 318 loop : -2.18 (0.15), residues: 1794 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2911 time to fit residues: 194.0871 Evaluate side-chains 314 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 264 optimal weight: 0.9990 chunk 282 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 254 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS A 730 HIS ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 23407 Z= 0.262 Angle : 0.650 14.368 31993 Z= 0.327 Chirality : 0.046 0.252 3832 Planarity : 0.005 0.078 4056 Dihedral : 5.374 54.296 3305 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.63 % Favored : 89.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.15), residues: 3122 helix: -0.35 (0.17), residues: 1007 sheet: -2.54 (0.27), residues: 320 loop : -2.22 (0.15), residues: 1795 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2889 time to fit residues: 182.2859 Evaluate side-chains 293 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 3.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 chunk 249 optimal weight: 0.0170 chunk 25 optimal weight: 9.9990 chunk 192 optimal weight: 0.5980 chunk 152 optimal weight: 9.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 23407 Z= 0.149 Angle : 0.586 12.707 31993 Z= 0.292 Chirality : 0.044 0.306 3832 Planarity : 0.004 0.078 4056 Dihedral : 4.841 54.257 3305 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.11 % Favored : 92.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.15), residues: 3122 helix: -0.21 (0.17), residues: 1009 sheet: -2.30 (0.29), residues: 303 loop : -2.11 (0.15), residues: 1810 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.532 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 outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2923 time to fit residues: 188.5696 Evaluate side-chains 303 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 40.0000 chunk 265 optimal weight: 40.0000 chunk 76 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 249 optimal weight: 0.0870 chunk 104 optimal weight: 7.9990 chunk 256 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.135535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115858 restraints weight = 64090.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118152 restraints weight = 41773.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119722 restraints weight = 31007.474| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 23407 Z= 0.179 Angle : 0.599 12.800 31993 Z= 0.297 Chirality : 0.044 0.321 3832 Planarity : 0.004 0.078 4056 Dihedral : 4.913 55.096 3305 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.81 % Favored : 91.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 3122 helix: -0.16 (0.17), residues: 1009 sheet: -2.46 (0.29), residues: 283 loop : -2.04 (0.15), residues: 1830 =============================================================================== Job complete usr+sys time: 4346.45 seconds wall clock time: 80 minutes 7.11 seconds (4807.11 seconds total)