Starting phenix.real_space_refine on Mon Nov 18 21:53:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/11_2024/8szg_40915.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/11_2024/8szg_40915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/11_2024/8szg_40915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/11_2024/8szg_40915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/11_2024/8szg_40915.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szg_40915/11_2024/8szg_40915.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.048 sd= 0.126 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 3 5.49 5 S 100 5.16 5 C 11359 2.51 5 N 2904 2.21 5 O 3196 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17571 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2404 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 142 Chain: "E" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 368 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 6520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6520 Classifications: {'peptide': 830} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 32, 'TRANS': 797} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 6279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6279 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 31, 'TRANS': 764} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1640 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 159 Unusual residues: {' CA': 3, 'NAG': 2, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1208 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 117 Unusual residues: {'CLR': 1, 'NAG': 2, 'PO4': 1, 'SPM': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1405 "'] Classifications: {'peptide': 1, 'undetermined': 6, 'water': 1} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.07, per 1000 atoms: 0.69 Number of scatterers: 17571 At special positions: 0 Unit cell: (102.389, 108.463, 251.633, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 100 16.00 P 3 15.00 F 6 9.00 O 3196 8.00 N 2904 7.00 C 11359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1202 " - " ASN A 287 " " NAG A1203 " - " ASN A 468 " " NAG B1402 " - " ASN B 468 " " NAG B1403 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.3 seconds 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4216 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 24 sheets defined 43.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.703A pdb=" N ALA D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 10 through 24 removed outlier: 3.647A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.626A pdb=" N HIS E 44 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.757A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.614A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.929A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.749A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.659A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.513A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.978A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 4.458A pdb=" N HIS A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.831A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.758A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.193A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.522A pdb=" N VAL A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.862A pdb=" N LEU A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.561A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 4.039A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 673 through 706 removed outlier: 5.064A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix Processing helix chain 'A' and resid 716 through 746 removed outlier: 3.606A pdb=" N LEU A 723 " --> pdb=" O TRP A 719 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.515A pdb=" N GLY A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 821 removed outlier: 3.565A pdb=" N LEU A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 removed outlier: 3.550A pdb=" N TYR A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 863 removed outlier: 3.844A pdb=" N PHE A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 867 Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.886A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.562A pdb=" N PHE B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.596A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.885A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.699A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.543A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.912A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 removed outlier: 3.524A pdb=" N SER B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.568A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 416 through 436 removed outlier: 3.544A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.547A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.557A pdb=" N ILE B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.855A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 666 removed outlier: 3.579A pdb=" N PHE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 673 through 698 removed outlier: 3.647A pdb=" N CYS B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix removed outlier: 3.512A pdb=" N ILE B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.514A pdb=" N PHE B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.774A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.688A pdb=" N ALA B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 826 removed outlier: 3.901A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 832 through 862 removed outlier: 3.606A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 36 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.539A pdb=" N GLN C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 233 through 236 removed outlier: 4.000A pdb=" N ASP C 236 " --> pdb=" O SER C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 246 through 261 removed outlier: 3.753A pdb=" N GLU C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 261 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 282 removed outlier: 4.004A pdb=" N LEU C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.577A pdb=" N TYR C 291 " --> pdb=" O HIS C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 removed outlier: 3.767A pdb=" N LEU C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 356 Processing sheet with id=AA1, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.351A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 337 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.945A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 72 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 80 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.590A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.804A pdb=" N CYS D 148 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.660A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 201 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.751A pdb=" N ALA D 231 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 253 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 251 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 252 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 273 through 278 removed outlier: 4.194A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL D 296 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.493A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 142 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.194A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 269 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.872A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 470 removed outlier: 3.636A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB4, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AB5, first strand: chain 'A' and resid 589 through 590 Processing sheet with id=AB6, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.189A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.635A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 142 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.051A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC2, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AC3, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.614A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 749 through 750 removed outlier: 3.786A pdb=" N SER B 749 " --> pdb=" O HIS B 766 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.648A pdb=" N LEU C 40 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 225 through 231 removed outlier: 5.970A pdb=" N ILE C 226 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE C 272 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 228 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN C 274 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 230 " --> pdb=" O ASN C 274 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2106 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: 6.44 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2955 1.32 - 1.46: 5579 1.46 - 1.59: 9309 1.59 - 1.72: 6 1.72 - 1.86: 127 Bond restraints: 17976 Sorted by residual: bond pdb=" C31 PCW A1204 " pdb=" O2 PCW A1204 " ideal model delta sigma weight residual 1.333 1.487 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" CG1 ILE C 337 " pdb=" CD1 ILE C 337 " ideal model delta sigma weight residual 1.513 1.267 0.246 3.90e-02 6.57e+02 3.96e+01 bond pdb=" C16 PCW A1204 " pdb=" C17 PCW A1204 " ideal model delta sigma weight residual 1.523 1.623 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C31 PCW A1204 " pdb=" C32 PCW A1204 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C11 PCW A1204 " pdb=" O3 PCW A1204 " ideal model delta sigma weight residual 1.326 1.417 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 17971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 24318 4.95 - 9.90: 75 9.90 - 14.84: 5 14.84 - 19.79: 1 19.79 - 24.74: 2 Bond angle restraints: 24401 Sorted by residual: angle pdb=" C PHE C 341 " pdb=" CA PHE C 341 " pdb=" CB PHE C 341 " ideal model delta sigma weight residual 110.85 88.88 21.97 1.70e+00 3.46e-01 1.67e+02 angle pdb=" C18 PCW A1204 " pdb=" C19 PCW A1204 " pdb=" C20 PCW A1204 " ideal model delta sigma weight residual 127.82 152.56 -24.74 3.00e+00 1.11e-01 6.80e+01 angle pdb=" C THR B 596 " pdb=" CA THR B 596 " pdb=" CB THR B 596 " ideal model delta sigma weight residual 110.88 98.18 12.70 1.57e+00 4.06e-01 6.54e+01 angle pdb=" N LYS C 345 " pdb=" CA LYS C 345 " pdb=" C LYS C 345 " ideal model delta sigma weight residual 111.07 103.21 7.86 1.07e+00 8.73e-01 5.40e+01 angle pdb=" N ILE B 434 " pdb=" CA ILE B 434 " pdb=" C ILE B 434 " ideal model delta sigma weight residual 110.72 103.40 7.32 1.01e+00 9.80e-01 5.25e+01 ... (remaining 24396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 10481 32.59 - 65.17: 266 65.17 - 97.76: 25 97.76 - 130.34: 1 130.34 - 162.93: 1 Dihedral angle restraints: 10774 sinusoidal: 4269 harmonic: 6505 Sorted by residual: dihedral pdb=" C PHE C 341 " pdb=" N PHE C 341 " pdb=" CA PHE C 341 " pdb=" CB PHE C 341 " ideal model delta harmonic sigma weight residual -122.60 -95.83 -26.77 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -176.09 90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual -86.00 -169.45 83.45 1 1.00e+01 1.00e-02 8.50e+01 ... (remaining 10771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.027: 2785 1.027 - 2.053: 0 2.053 - 3.080: 0 3.080 - 4.107: 0 4.107 - 5.133: 1 Chirality restraints: 2786 Sorted by residual: chirality pdb=" C2 PCW A1204 " pdb=" C1 PCW A1204 " pdb=" C3 PCW A1204 " pdb=" O2 PCW A1204 " both_signs ideal model delta sigma weight residual False -2.32 2.81 -5.13 2.00e-01 2.50e+01 6.59e+02 chirality pdb=" CA ASP C 346 " pdb=" N ASP C 346 " pdb=" C ASP C 346 " pdb=" CB ASP C 346 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.48e+01 ... (remaining 2783 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 821 " -0.044 2.00e-02 2.50e+03 4.41e-02 3.40e+01 pdb=" CG PHE B 821 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE B 821 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 PHE B 821 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE B 821 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE B 821 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 821 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 792 " 0.030 2.00e-02 2.50e+03 3.97e-02 2.75e+01 pdb=" CG PHE B 792 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 792 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 PHE B 792 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE B 792 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE B 792 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 792 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 712 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C THR A 712 " -0.073 2.00e-02 2.50e+03 pdb=" O THR A 712 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 713 " 0.024 2.00e-02 2.50e+03 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4758 2.80 - 3.33: 15600 3.33 - 3.85: 26727 3.85 - 4.38: 30397 4.38 - 4.90: 53679 Nonbonded interactions: 131161 Sorted by model distance: nonbonded pdb=" OG1 THR B 550 " pdb=" O VAL B 566 " model vdw 2.281 3.040 nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR D 102 " pdb=" O SER D 147 " model vdw 2.308 3.040 nonbonded pdb=" OE1 GLU B 229 " pdb=" NH1 ARG B 233 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG B 69 " pdb=" O2 PO4 B1406 " model vdw 2.326 3.120 ... (remaining 131156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 118 or (resid 119 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 546 or (resid 547 through 548 and (name N \ or name CA or name C or name O or name CB )) or resid 549 through 586 or (resid \ 587 through 588 and (name N or name CA or name C or name O or name CB )) or resi \ d 589 through 673 or (resid 674 and (name N or name CA or name C or name O or na \ me CB )) or resid 675 through 707 or resid 722 through 734 or (resid 735 and (na \ me N or name CA or name C or name O or name CB )) or resid 736 through 756 or (r \ esid 757 and (name N or name CA or name C or name O or name CB )) or resid 758 t \ hrough 801 or (resid 802 and (name N or name CA or name C or name O or name CB ) \ ) or resid 803 through 868 or (resid 869 through 871 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1208 through 1209)) selection = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 120 or (resid 134 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 360 or \ (resid 361 through 362 and (name N or name CA or name C or name O or name CB )) \ or resid 392 through 480 or (resid 481 and (name N or name CA or name C or name \ O or name CB )) or resid 482 through 498 or (resid 499 through 500 and (name N \ or name CA or name C or name O or name CB )) or resid 501 through 591 or (resid \ 592 through 593 and (name N or name CA or name C or name O or name CB )) or resi \ d 594 through 608 or (resid 609 through 610 and (name N or name CA or name C or \ name O or name CB )) or resid 611 through 670 or (resid 671 and (name N or name \ CA or name C or name O or name CB )) or resid 672 through 706 or (resid 707 thro \ ugh 722 and (name N or name CA or name C or name O or name CB )) or resid 723 th \ rough 871 or resid 1405 through 1406)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 7.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.120 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.006 0.246 17976 Z= 0.400 Angle : 0.851 24.740 24401 Z= 0.519 Chirality : 0.114 5.133 2786 Planarity : 0.005 0.050 3061 Dihedral : 14.080 162.926 6504 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2209 helix: 0.79 (0.18), residues: 869 sheet: -0.76 (0.29), residues: 347 loop : -1.25 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 742 HIS 0.010 0.001 HIS A 879 PHE 0.085 0.003 PHE B 821 TYR 0.031 0.002 TYR B 829 ARG 0.018 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8753 (mppt) cc_final: 0.8405 (mmtm) REVERT: D 63 TRP cc_start: 0.7781 (m100) cc_final: 0.7371 (m100) REVERT: A 790 PHE cc_start: 0.8329 (m-10) cc_final: 0.7984 (m-80) REVERT: A 832 PHE cc_start: 0.6995 (m-10) cc_final: 0.6712 (m-80) REVERT: B 510 TYR cc_start: 0.8072 (p90) cc_final: 0.7869 (p90) REVERT: B 558 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 618 LEU cc_start: 0.7929 (mt) cc_final: 0.7534 (pp) REVERT: B 738 ILE cc_start: 0.7575 (tp) cc_final: 0.7296 (tt) REVERT: C 29 LEU cc_start: 0.8964 (tp) cc_final: 0.8689 (tt) REVERT: C 44 LEU cc_start: 0.7931 (tp) cc_final: 0.7509 (tp) REVERT: C 259 ILE cc_start: 0.8241 (mm) cc_final: 0.7756 (tt) REVERT: C 282 LYS cc_start: 0.7408 (mtpt) cc_final: 0.7189 (mtpp) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.3189 time to fit residues: 145.3610 Evaluate side-chains 240 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 173 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 200 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 471 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17976 Z= 0.168 Angle : 0.550 9.263 24401 Z= 0.291 Chirality : 0.043 0.252 2786 Planarity : 0.004 0.043 3061 Dihedral : 8.724 84.207 2762 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.01 % Allowed : 8.61 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2209 helix: 1.40 (0.18), residues: 877 sheet: -0.59 (0.28), residues: 367 loop : -1.31 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 818 HIS 0.008 0.001 HIS B 359 PHE 0.019 0.001 PHE A 814 TYR 0.020 0.001 TYR D 111 ARG 0.007 0.000 ARG E 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8765 (mppt) cc_final: 0.8419 (mmtm) REVERT: D 63 TRP cc_start: 0.7733 (m100) cc_final: 0.7348 (m100) REVERT: A 446 ASN cc_start: 0.7486 (m110) cc_final: 0.7274 (m-40) REVERT: A 760 ILE cc_start: 0.8624 (mt) cc_final: 0.8282 (mm) REVERT: A 789 PHE cc_start: 0.8532 (t80) cc_final: 0.8212 (t80) REVERT: A 790 PHE cc_start: 0.8023 (m-10) cc_final: 0.7670 (m-80) REVERT: A 829 TYR cc_start: 0.7978 (p90) cc_final: 0.7636 (p90) REVERT: A 832 PHE cc_start: 0.6987 (m-10) cc_final: 0.6708 (m-80) REVERT: B 446 ASN cc_start: 0.7797 (t0) cc_final: 0.7562 (t0) REVERT: B 558 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 852 ILE cc_start: 0.8463 (mt) cc_final: 0.8231 (mm) REVERT: C 29 LEU cc_start: 0.8929 (tp) cc_final: 0.8670 (tt) REVERT: C 252 LYS cc_start: 0.7305 (mtpp) cc_final: 0.6963 (mtpp) REVERT: C 259 ILE cc_start: 0.8063 (mm) cc_final: 0.7384 (pt) REVERT: C 316 LEU cc_start: 0.8062 (tt) cc_final: 0.7747 (mt) REVERT: C 321 ASP cc_start: 0.7008 (t0) cc_final: 0.6769 (t0) outliers start: 18 outliers final: 9 residues processed: 258 average time/residue: 0.3188 time to fit residues: 123.7806 Evaluate side-chains 241 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 232 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 815 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 167 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 700 ASN B 800 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17976 Z= 0.150 Angle : 0.504 11.287 24401 Z= 0.264 Chirality : 0.042 0.230 2786 Planarity : 0.004 0.052 3061 Dihedral : 8.083 85.032 2761 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.29 % Allowed : 10.34 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2209 helix: 1.57 (0.18), residues: 881 sheet: -0.61 (0.28), residues: 373 loop : -1.25 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 818 HIS 0.006 0.001 HIS B 359 PHE 0.014 0.001 PHE A 814 TYR 0.013 0.001 TYR D 111 ARG 0.006 0.000 ARG A 873 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8779 (mppt) cc_final: 0.8486 (mmtm) REVERT: D 63 TRP cc_start: 0.7731 (m100) cc_final: 0.7346 (m100) REVERT: D 234 PHE cc_start: 0.5373 (t80) cc_final: 0.5005 (t80) REVERT: A 760 ILE cc_start: 0.8611 (mt) cc_final: 0.8303 (mm) REVERT: A 790 PHE cc_start: 0.8011 (m-10) cc_final: 0.7722 (m-10) REVERT: A 829 TYR cc_start: 0.7967 (p90) cc_final: 0.7714 (p90) REVERT: A 832 PHE cc_start: 0.6889 (m-10) cc_final: 0.6642 (m-80) REVERT: B 446 ASN cc_start: 0.7812 (t0) cc_final: 0.7459 (t0) REVERT: B 558 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7609 (mm-30) REVERT: C 27 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7548 (ttp-170) REVERT: C 29 LEU cc_start: 0.8925 (tp) cc_final: 0.8667 (tt) REVERT: C 212 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6905 (mm-30) REVERT: C 252 LYS cc_start: 0.7248 (mtpp) cc_final: 0.6729 (mtmm) REVERT: C 259 ILE cc_start: 0.8050 (mm) cc_final: 0.7370 (pt) REVERT: C 312 MET cc_start: 0.8289 (tpp) cc_final: 0.7819 (tmm) outliers start: 23 outliers final: 13 residues processed: 250 average time/residue: 0.3361 time to fit residues: 126.5111 Evaluate side-chains 241 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 228 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 201 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17976 Z= 0.182 Angle : 0.499 9.496 24401 Z= 0.263 Chirality : 0.042 0.230 2786 Planarity : 0.004 0.043 3061 Dihedral : 7.627 77.557 2761 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.45 % Allowed : 11.24 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2209 helix: 1.61 (0.18), residues: 883 sheet: -0.61 (0.29), residues: 351 loop : -1.27 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.019 0.001 PHE A 625 TYR 0.012 0.001 TYR B 751 ARG 0.006 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8790 (mppt) cc_final: 0.8487 (mmtm) REVERT: D 63 TRP cc_start: 0.7774 (m100) cc_final: 0.7405 (m100) REVERT: D 234 PHE cc_start: 0.5308 (t80) cc_final: 0.4980 (t80) REVERT: A 760 ILE cc_start: 0.8619 (mt) cc_final: 0.8259 (mm) REVERT: A 790 PHE cc_start: 0.8008 (m-10) cc_final: 0.7693 (m-80) REVERT: A 829 TYR cc_start: 0.7955 (p90) cc_final: 0.7731 (p90) REVERT: A 832 PHE cc_start: 0.6943 (m-10) cc_final: 0.6719 (m-80) REVERT: B 446 ASN cc_start: 0.7858 (t0) cc_final: 0.7471 (t0) REVERT: B 558 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 29 LEU cc_start: 0.8932 (tp) cc_final: 0.8720 (tt) REVERT: C 212 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7256 (mm-30) REVERT: C 259 ILE cc_start: 0.8033 (mm) cc_final: 0.7304 (pt) outliers start: 26 outliers final: 22 residues processed: 246 average time/residue: 0.3152 time to fit residues: 116.3815 Evaluate side-chains 247 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 182 optimal weight: 0.2980 chunk 147 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17976 Z= 0.152 Angle : 0.490 13.236 24401 Z= 0.255 Chirality : 0.041 0.228 2786 Planarity : 0.003 0.044 3061 Dihedral : 7.076 75.853 2761 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.73 % Allowed : 12.58 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2209 helix: 1.71 (0.18), residues: 877 sheet: -0.60 (0.29), residues: 356 loop : -1.27 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.027 0.001 PHE B 789 TYR 0.013 0.001 TYR B 744 ARG 0.005 0.000 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 ARG cc_start: 0.7876 (mpt180) cc_final: 0.7596 (mpt180) REVERT: D 57 LYS cc_start: 0.8777 (mppt) cc_final: 0.8508 (mmtm) REVERT: D 63 TRP cc_start: 0.7748 (m100) cc_final: 0.7378 (m100) REVERT: D 234 PHE cc_start: 0.5329 (t80) cc_final: 0.5035 (t80) REVERT: D 334 SER cc_start: 0.6495 (p) cc_final: 0.6067 (p) REVERT: A 719 TRP cc_start: 0.6827 (t60) cc_final: 0.6236 (t-100) REVERT: A 760 ILE cc_start: 0.8616 (mt) cc_final: 0.8316 (mm) REVERT: A 790 PHE cc_start: 0.8011 (m-10) cc_final: 0.7618 (m-80) REVERT: A 832 PHE cc_start: 0.6888 (m-10) cc_final: 0.6682 (m-80) REVERT: B 446 ASN cc_start: 0.7857 (t0) cc_final: 0.7580 (t0) REVERT: B 558 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7669 (mm-30) REVERT: C 29 LEU cc_start: 0.8929 (tp) cc_final: 0.8717 (tt) REVERT: C 212 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7196 (mm-30) REVERT: C 259 ILE cc_start: 0.8051 (mm) cc_final: 0.7326 (pt) REVERT: C 311 LYS cc_start: 0.7853 (tmtt) cc_final: 0.7462 (tmtt) REVERT: C 315 ASP cc_start: 0.7955 (p0) cc_final: 0.7577 (p0) outliers start: 31 outliers final: 25 residues processed: 253 average time/residue: 0.3075 time to fit residues: 117.9460 Evaluate side-chains 244 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 316 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.2980 chunk 192 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 218 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17976 Z= 0.170 Angle : 0.494 13.525 24401 Z= 0.258 Chirality : 0.041 0.230 2786 Planarity : 0.003 0.044 3061 Dihedral : 6.766 74.686 2761 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.07 % Allowed : 13.25 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2209 helix: 1.69 (0.18), residues: 885 sheet: -0.61 (0.29), residues: 351 loop : -1.22 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.028 0.001 PHE B 789 TYR 0.013 0.001 TYR B 751 ARG 0.006 0.000 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8781 (mppt) cc_final: 0.8515 (mmtm) REVERT: D 63 TRP cc_start: 0.7788 (m100) cc_final: 0.7397 (m100) REVERT: D 234 PHE cc_start: 0.5374 (t80) cc_final: 0.5096 (t80) REVERT: D 334 SER cc_start: 0.6473 (p) cc_final: 0.6036 (p) REVERT: E 21 MET cc_start: 0.7399 (ppp) cc_final: 0.6597 (ttp) REVERT: A 719 TRP cc_start: 0.6842 (t60) cc_final: 0.6252 (t-100) REVERT: A 760 ILE cc_start: 0.8621 (mt) cc_final: 0.8345 (mm) REVERT: A 790 PHE cc_start: 0.8017 (m-10) cc_final: 0.7662 (m-80) REVERT: A 832 PHE cc_start: 0.6923 (m-10) cc_final: 0.6706 (m-80) REVERT: B 446 ASN cc_start: 0.7847 (t0) cc_final: 0.7555 (t0) REVERT: B 558 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 854 PHE cc_start: 0.7154 (m-80) cc_final: 0.6918 (m-80) REVERT: C 29 LEU cc_start: 0.8935 (tp) cc_final: 0.8721 (tt) REVERT: C 203 MET cc_start: 0.7295 (mmt) cc_final: 0.7052 (mmt) REVERT: C 212 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7222 (mm-30) REVERT: C 252 LYS cc_start: 0.7204 (mtpp) cc_final: 0.6948 (mtmm) REVERT: C 259 ILE cc_start: 0.8011 (mm) cc_final: 0.7300 (pt) outliers start: 37 outliers final: 29 residues processed: 245 average time/residue: 0.3023 time to fit residues: 113.1900 Evaluate side-chains 252 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 316 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17976 Z= 0.155 Angle : 0.491 13.615 24401 Z= 0.255 Chirality : 0.041 0.229 2786 Planarity : 0.003 0.044 3061 Dihedral : 6.586 73.378 2761 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.18 % Allowed : 13.42 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2209 helix: 1.71 (0.18), residues: 885 sheet: -0.57 (0.29), residues: 351 loop : -1.23 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 530 HIS 0.010 0.001 HIS C 218 PHE 0.029 0.001 PHE B 789 TYR 0.016 0.001 TYR B 751 ARG 0.004 0.000 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8788 (mppt) cc_final: 0.8512 (mmtm) REVERT: D 63 TRP cc_start: 0.7771 (m100) cc_final: 0.7400 (m100) REVERT: D 334 SER cc_start: 0.6439 (p) cc_final: 0.6010 (p) REVERT: A 719 TRP cc_start: 0.6860 (t60) cc_final: 0.6230 (t-100) REVERT: A 760 ILE cc_start: 0.8625 (mt) cc_final: 0.8360 (mm) REVERT: A 790 PHE cc_start: 0.8023 (m-10) cc_final: 0.7642 (m-80) REVERT: A 832 PHE cc_start: 0.6893 (m-10) cc_final: 0.6675 (m-80) REVERT: B 446 ASN cc_start: 0.7862 (t0) cc_final: 0.7559 (t0) REVERT: B 558 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 854 PHE cc_start: 0.7184 (m-80) cc_final: 0.6956 (m-80) REVERT: C 29 LEU cc_start: 0.8936 (tp) cc_final: 0.8715 (tt) REVERT: C 203 MET cc_start: 0.7290 (mmt) cc_final: 0.7065 (mmt) REVERT: C 259 ILE cc_start: 0.7990 (mm) cc_final: 0.7298 (pt) outliers start: 39 outliers final: 31 residues processed: 252 average time/residue: 0.3056 time to fit residues: 117.4587 Evaluate side-chains 261 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 316 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 135 optimal weight: 0.0070 chunk 145 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17976 Z= 0.167 Angle : 0.505 13.381 24401 Z= 0.263 Chirality : 0.041 0.229 2786 Planarity : 0.003 0.044 3061 Dihedral : 6.428 71.986 2761 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.18 % Allowed : 13.47 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2209 helix: 1.73 (0.18), residues: 880 sheet: -0.59 (0.29), residues: 351 loop : -1.23 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 263 HIS 0.004 0.001 HIS B 359 PHE 0.032 0.001 PHE B 789 TYR 0.015 0.001 TYR B 751 ARG 0.004 0.000 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8784 (mppt) cc_final: 0.8509 (mmtm) REVERT: D 63 TRP cc_start: 0.7781 (m100) cc_final: 0.7390 (m100) REVERT: D 334 SER cc_start: 0.6411 (p) cc_final: 0.5974 (p) REVERT: E 21 MET cc_start: 0.7347 (ppp) cc_final: 0.6616 (ttp) REVERT: A 719 TRP cc_start: 0.6844 (t60) cc_final: 0.6204 (t-100) REVERT: A 760 ILE cc_start: 0.8635 (mt) cc_final: 0.8365 (mm) REVERT: A 790 PHE cc_start: 0.8007 (m-10) cc_final: 0.7631 (m-80) REVERT: A 832 PHE cc_start: 0.6872 (m-10) cc_final: 0.6626 (m-80) REVERT: B 446 ASN cc_start: 0.7845 (t0) cc_final: 0.7543 (t0) REVERT: B 558 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 854 PHE cc_start: 0.7315 (m-80) cc_final: 0.7052 (m-80) REVERT: C 29 LEU cc_start: 0.8942 (tp) cc_final: 0.8722 (tt) REVERT: C 212 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7376 (mm-30) REVERT: C 259 ILE cc_start: 0.7974 (mm) cc_final: 0.7295 (pt) outliers start: 39 outliers final: 31 residues processed: 251 average time/residue: 0.3109 time to fit residues: 118.9597 Evaluate side-chains 260 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 0.0000 chunk 60 optimal weight: 0.5980 chunk 179 optimal weight: 0.0000 chunk 187 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 218 HIS C 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17976 Z= 0.146 Angle : 0.497 13.463 24401 Z= 0.257 Chirality : 0.041 0.229 2786 Planarity : 0.003 0.044 3061 Dihedral : 6.124 69.602 2761 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.96 % Allowed : 13.81 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2209 helix: 1.81 (0.18), residues: 876 sheet: -0.59 (0.28), residues: 365 loop : -1.22 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 530 HIS 0.004 0.001 HIS B 359 PHE 0.039 0.001 PHE B 789 TYR 0.013 0.001 TYR B 751 ARG 0.004 0.000 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 ARG cc_start: 0.7838 (mpt180) cc_final: 0.7195 (mmm160) REVERT: D 57 LYS cc_start: 0.8785 (mppt) cc_final: 0.8516 (mmtm) REVERT: D 63 TRP cc_start: 0.7765 (m100) cc_final: 0.7357 (m100) REVERT: D 139 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6922 (mt) REVERT: D 334 SER cc_start: 0.6363 (p) cc_final: 0.5931 (p) REVERT: E 13 ARG cc_start: 0.7404 (tpm170) cc_final: 0.7162 (tpt90) REVERT: E 21 MET cc_start: 0.7365 (ppp) cc_final: 0.6687 (ttp) REVERT: A 719 TRP cc_start: 0.6756 (t60) cc_final: 0.6135 (t-100) REVERT: A 745 THR cc_start: 0.8326 (t) cc_final: 0.7997 (t) REVERT: A 760 ILE cc_start: 0.8635 (mt) cc_final: 0.8362 (mm) REVERT: A 790 PHE cc_start: 0.7978 (m-10) cc_final: 0.7623 (m-80) REVERT: A 832 PHE cc_start: 0.6826 (m-10) cc_final: 0.6582 (m-80) REVERT: B 446 ASN cc_start: 0.7886 (t0) cc_final: 0.7372 (t0) REVERT: B 558 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 854 PHE cc_start: 0.7286 (m-80) cc_final: 0.7059 (m-80) REVERT: C 29 LEU cc_start: 0.8942 (tp) cc_final: 0.8722 (tt) REVERT: C 212 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7351 (mm-30) REVERT: C 259 ILE cc_start: 0.7917 (mm) cc_final: 0.7258 (pt) outliers start: 35 outliers final: 27 residues processed: 248 average time/residue: 0.3103 time to fit residues: 117.6390 Evaluate side-chains 259 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 0.0370 chunk 128 optimal weight: 0.8980 chunk 99 optimal weight: 0.0050 chunk 145 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.4872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17976 Z= 0.149 Angle : 0.503 12.985 24401 Z= 0.260 Chirality : 0.041 0.229 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.020 68.244 2761 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.84 % Allowed : 13.97 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2209 helix: 1.81 (0.18), residues: 879 sheet: -0.59 (0.28), residues: 365 loop : -1.20 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 169 HIS 0.004 0.001 HIS B 359 PHE 0.032 0.001 PHE B 789 TYR 0.024 0.001 TYR E 40 ARG 0.004 0.000 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 ARG cc_start: 0.7858 (mpt180) cc_final: 0.7213 (mmm160) REVERT: D 57 LYS cc_start: 0.8795 (mppt) cc_final: 0.8533 (mmtm) REVERT: D 63 TRP cc_start: 0.7780 (m100) cc_final: 0.7413 (m100) REVERT: D 139 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6912 (mt) REVERT: D 334 SER cc_start: 0.6345 (p) cc_final: 0.5914 (p) REVERT: E 13 ARG cc_start: 0.7442 (tpm170) cc_final: 0.7203 (tpt90) REVERT: E 21 MET cc_start: 0.7368 (ppp) cc_final: 0.6707 (ttp) REVERT: A 719 TRP cc_start: 0.6756 (t60) cc_final: 0.6159 (t-100) REVERT: A 745 THR cc_start: 0.8262 (t) cc_final: 0.7942 (t) REVERT: A 760 ILE cc_start: 0.8636 (mt) cc_final: 0.8361 (mm) REVERT: A 790 PHE cc_start: 0.7964 (m-10) cc_final: 0.7621 (m-80) REVERT: A 832 PHE cc_start: 0.6809 (m-10) cc_final: 0.6565 (m-80) REVERT: B 446 ASN cc_start: 0.7862 (t0) cc_final: 0.7423 (t0) REVERT: B 558 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 854 PHE cc_start: 0.7314 (m-80) cc_final: 0.7045 (m-80) REVERT: C 29 LEU cc_start: 0.8949 (tp) cc_final: 0.8727 (tt) REVERT: C 212 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7397 (mm-30) REVERT: C 259 ILE cc_start: 0.7935 (mm) cc_final: 0.7280 (pt) outliers start: 33 outliers final: 28 residues processed: 246 average time/residue: 0.3215 time to fit residues: 120.6286 Evaluate side-chains 263 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 154 optimal weight: 0.0670 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.088975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072556 restraints weight = 50015.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072983 restraints weight = 42832.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073638 restraints weight = 35704.447| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17976 Z= 0.158 Angle : 0.505 12.461 24401 Z= 0.260 Chirality : 0.041 0.229 2786 Planarity : 0.003 0.044 3061 Dihedral : 5.944 66.366 2761 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.73 % Allowed : 14.14 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2209 helix: 1.83 (0.18), residues: 879 sheet: -0.58 (0.28), residues: 365 loop : -1.19 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 818 HIS 0.004 0.001 HIS B 359 PHE 0.037 0.001 PHE B 789 TYR 0.021 0.001 TYR E 40 ARG 0.004 0.000 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.86 seconds wall clock time: 68 minutes 3.04 seconds (4083.04 seconds total)