Starting phenix.real_space_refine on Mon Mar 18 05:05:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfl_33792/03_2024/7yfl_33792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfl_33792/03_2024/7yfl_33792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfl_33792/03_2024/7yfl_33792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfl_33792/03_2024/7yfl_33792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfl_33792/03_2024/7yfl_33792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfl_33792/03_2024/7yfl_33792.pdb" } resolution = 3.9 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= 0.006 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 12720 2.51 5 N 3436 2.21 5 O 3722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 901": "OE1" <-> "OE2" Residue "D GLU 901": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19968 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5036 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 30, 'TRANS': 677} Chain breaks: 13 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 351 Chain: "B" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 4807 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 31, 'TRANS': 647} Chain breaks: 12 Unresolved non-hydrogen bonds: 535 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 15, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 340 Chain: "C" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5036 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 30, 'TRANS': 677} Chain breaks: 13 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 351 Chain: "D" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 4807 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 31, 'TRANS': 647} Chain breaks: 12 Unresolved non-hydrogen bonds: 535 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 15, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 340 Chain: "E" 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: "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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 11.09, per 1000 atoms: 0.56 Number of scatterers: 19968 At special positions: 0 Unit cell: (117.66, 143.1, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3722 8.00 N 3436 7.00 C 12720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 484 " distance=2.02 Simple disulfide: pdb=" SG CYS B 773 " - pdb=" SG CYS B 828 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 484 " distance=2.02 Simple disulfide: pdb=" SG CYS D 773 " - pdb=" SG CYS D 828 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 902 " - " ASN A 61 " " NAG A 903 " - " ASN A 471 " " NAG A 904 " - " ASN A 440 " " NAG A 905 " - " ASN A 368 " " NAG A 906 " - " ASN A 203 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 368 " " NAG C 904 " - " ASN C 440 " " NAG C 905 " - " ASN C 61 " " NAG C 906 " - " ASN C 471 " " NAG E 1 " - " ASN A 771 " " NAG F 1 " - " ASN B 715 " " NAG G 1 " - " ASN C 771 " " NAG H 1 " - " ASN D 715 " Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 3.8 seconds 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5188 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 24 sheets defined 43.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.782A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.409A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.768A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.636A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.915A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.793A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.639A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.806A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 4.550A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.675A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 580 removed outlier: 7.543A pdb=" N SER A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR A 561 " --> pdb=" O PRO A 557 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.646A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 656 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 693 Processing helix chain 'A' and resid 694 through 695 No H-bonds generated for 'chain 'A' and resid 694 through 695' Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.774A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.566A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 744 removed outlier: 4.265A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 782 removed outlier: 4.757A pdb=" N ASN A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.980A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.844A pdb=" N ALA B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.620A pdb=" N LEU B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 230 through 239 removed outlier: 4.046A pdb=" N VAL B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 263 removed outlier: 4.045A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 315 through 338 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 582 through 593 removed outlier: 4.492A pdb=" N TRP B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS B 593 " --> pdb=" O MET B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 removed outlier: 3.532A pdb=" N ASN B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 3.900A pdb=" N MET B 658 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 717 through 726 Processing helix chain 'B' and resid 730 through 734 removed outlier: 4.133A pdb=" N VAL B 734 " --> pdb=" O SER B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 750 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 799 through 813 removed outlier: 3.714A pdb=" N ASP B 804 " --> pdb=" O LYS B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 840 through 853 Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.782A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 84 Processing helix chain 'C' and resid 103 through 115 removed outlier: 4.311A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.790A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.631A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.755A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.794A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.640A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.784A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 4.551A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.675A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 580 removed outlier: 3.909A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 613 removed outlier: 3.645A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 656 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 693 Processing helix chain 'C' and resid 694 through 695 No H-bonds generated for 'chain 'C' and resid 694 through 695' Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 709 removed outlier: 3.773A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 723 removed outlier: 3.553A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 744 removed outlier: 4.266A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 782 removed outlier: 4.770A pdb=" N ASN C 771 " --> pdb=" O PRO C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.983A pdb=" N LEU D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.879A pdb=" N ALA D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 111 Processing helix chain 'D' and resid 126 through 137 removed outlier: 3.622A pdb=" N LEU D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 230 through 239 removed outlier: 4.043A pdb=" N VAL D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 263 removed outlier: 4.045A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 315 through 338 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 487 through 500 Processing helix chain 'D' and resid 522 through 530 Processing helix chain 'D' and resid 543 through 550 Processing helix chain 'D' and resid 582 through 593 removed outlier: 4.491A pdb=" N TRP D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS D 593 " --> pdb=" O MET D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 removed outlier: 3.536A pdb=" N ASN D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 682 removed outlier: 3.930A pdb=" N MET D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 717 through 726 Processing helix chain 'D' and resid 730 through 734 removed outlier: 4.133A pdb=" N VAL D 734 " --> pdb=" O SER D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 750 Processing helix chain 'D' and resid 761 through 766 Processing helix chain 'D' and resid 799 through 813 removed outlier: 3.718A pdb=" N ASP D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 824 Processing helix chain 'D' and resid 840 through 853 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.370A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 197 removed outlier: 6.312A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.228A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 513 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 761 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.696A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 485 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.744A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.134A pdb=" N ILE B 141 " --> pdb=" O LEU B 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.523A pdb=" N ARG B 244 " --> pdb=" O PHE B 273 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TRP B 272 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL B 307 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N MET B 274 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N SER B 309 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU B 304 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER B 391 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 400 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 367 through 369 Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 434 removed outlier: 6.973A pdb=" N VAL B 434 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B 505 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 463 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 755 through 758 removed outlier: 3.745A pdb=" N LEU B 775 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 755 through 758 removed outlier: 4.960A pdb=" N ILE B 561 " --> pdb=" O ALA B 785 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA B 785 " --> pdb=" O ILE B 561 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.386A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.306A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.229A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 512 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 513 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 761 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.723A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 485 through 489 Processing sheet with id=AB9, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.742A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 141 through 142 removed outlier: 6.131A pdb=" N ILE D 141 " --> pdb=" O LEU D 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 243 through 246 removed outlier: 6.522A pdb=" N ARG D 244 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TRP D 272 " --> pdb=" O PHE D 305 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL D 307 " --> pdb=" O TRP D 272 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET D 274 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N SER D 309 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER D 391 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL D 400 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 367 through 369 Processing sheet with id=AC4, first strand: chain 'D' and resid 433 through 434 removed outlier: 6.972A pdb=" N VAL D 434 " --> pdb=" O TYR D 506 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU D 505 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG D 463 " --> pdb=" O LEU D 505 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 755 through 758 removed outlier: 3.745A pdb=" N LEU D 775 " --> pdb=" O VAL D 565 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 755 through 758 removed outlier: 4.943A pdb=" N ILE D 561 " --> pdb=" O ALA D 785 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA D 785 " --> pdb=" O ILE D 561 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2442 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: 6.59 Time building geometry restraints manager: 9.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6555 1.34 - 1.47: 4868 1.47 - 1.59: 8783 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 20350 Sorted by residual: bond pdb=" N GLU A 662 " pdb=" CA GLU A 662 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.34e+00 bond pdb=" N GLU C 661 " pdb=" CA GLU C 661 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.13e-02 7.83e+03 5.35e+00 bond pdb=" CA THR C 665 " pdb=" C THR C 665 " ideal model delta sigma weight residual 1.522 1.493 0.029 1.31e-02 5.83e+03 4.75e+00 bond pdb=" N GLU C 662 " pdb=" CA GLU C 662 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.33e+00 bond pdb=" C1 NAG C 904 " pdb=" O5 NAG C 904 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 ... (remaining 20345 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.09: 484 106.09 - 113.08: 11377 113.08 - 120.07: 6462 120.07 - 127.06: 9208 127.06 - 134.05: 247 Bond angle restraints: 27778 Sorted by residual: angle pdb=" C ASP A 441 " pdb=" CA ASP A 441 " pdb=" CB ASP A 441 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.61e+01 angle pdb=" C TRP A 56 " pdb=" CA TRP A 56 " pdb=" CB TRP A 56 " ideal model delta sigma weight residual 115.79 110.29 5.50 1.19e+00 7.06e-01 2.14e+01 angle pdb=" CA LYS B 782 " pdb=" CB LYS B 782 " pdb=" CG LYS B 782 " ideal model delta sigma weight residual 114.10 122.39 -8.29 2.00e+00 2.50e-01 1.72e+01 angle pdb=" CA TRP C 636 " pdb=" CB TRP C 636 " pdb=" CG TRP C 636 " ideal model delta sigma weight residual 113.60 120.90 -7.30 1.90e+00 2.77e-01 1.48e+01 angle pdb=" CA TRP A 636 " pdb=" CB TRP A 636 " pdb=" CG TRP A 636 " ideal model delta sigma weight residual 113.60 120.81 -7.21 1.90e+00 2.77e-01 1.44e+01 ... (remaining 27773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 10969 21.17 - 42.34: 995 42.34 - 63.50: 212 63.50 - 84.67: 24 84.67 - 105.84: 12 Dihedral angle restraints: 12212 sinusoidal: 4220 harmonic: 7992 Sorted by residual: dihedral pdb=" CB CYS D 462 " pdb=" SG CYS D 462 " pdb=" SG CYS D 484 " pdb=" CB CYS D 484 " ideal model delta sinusoidal sigma weight residual -86.00 -174.19 88.19 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS B 462 " pdb=" SG CYS B 462 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -173.97 87.97 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS D 455 " pdb=" SG CYS D 455 " pdb=" SG CYS D 483 " pdb=" CB CYS D 483 " ideal model delta sinusoidal sigma weight residual 93.00 154.50 -61.50 1 1.00e+01 1.00e-02 5.02e+01 ... (remaining 12209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3072 0.081 - 0.162: 259 0.162 - 0.243: 1 0.243 - 0.324: 4 0.324 - 0.404: 2 Chirality restraints: 3338 Sorted by residual: chirality pdb=" C1 NAG C 904 " pdb=" ND2 ASN C 440 " pdb=" C2 NAG C 904 " pdb=" O5 NAG C 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C1 NAG C 905 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C 905 " pdb=" O5 NAG C 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CG LEU D 670 " pdb=" CB LEU D 670 " pdb=" CD1 LEU D 670 " pdb=" CD2 LEU D 670 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3335 not shown) Planarity restraints: 3564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 440 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO B 441 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO B 441 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 441 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 440 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO D 441 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO D 441 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 441 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 636 " -0.031 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP C 636 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP C 636 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 636 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 636 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 636 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 636 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 636 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 636 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 636 " 0.000 2.00e-02 2.50e+03 ... (remaining 3561 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4924 2.79 - 3.32: 19190 3.32 - 3.84: 31379 3.84 - 4.37: 32286 4.37 - 4.90: 56166 Nonbonded interactions: 143945 Sorted by model distance: nonbonded pdb=" NH2 ARG A 397 " pdb=" OE1 GLU A 475 " model vdw 2.260 2.520 nonbonded pdb=" NH2 ARG C 397 " pdb=" OE1 GLU C 475 " model vdw 2.261 2.520 nonbonded pdb=" OH TYR C 114 " pdb=" O CYS C 308 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR A 114 " pdb=" O CYS A 308 " model vdw 2.267 2.440 nonbonded pdb=" O SER C 446 " pdb=" OG SER C 446 " model vdw 2.277 2.440 ... (remaining 143940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = 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: 1.000 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: 4.940 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 54.530 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.005 0.046 20350 Z= 0.303 Angle : 0.638 9.250 27778 Z= 0.326 Chirality : 0.044 0.404 3338 Planarity : 0.005 0.121 3550 Dihedral : 16.695 105.838 6982 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.88 % Favored : 91.79 % Rotamer: Outliers : 0.34 % Allowed : 31.71 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2666 helix: 1.78 (0.17), residues: 1048 sheet: -1.63 (0.36), residues: 242 loop : -1.86 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP C 636 HIS 0.006 0.001 HIS C 780 PHE 0.019 0.002 PHE A 113 TYR 0.020 0.001 TYR B 673 ARG 0.005 0.000 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 2.342 Fit side-chains REVERT: C 679 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.6190 (t80) outliers start: 6 outliers final: 4 residues processed: 173 average time/residue: 0.2622 time to fit residues: 75.5615 Evaluate side-chains 168 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain D residue 520 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 7.9990 chunk 207 optimal weight: 0.0040 chunk 115 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 140 optimal weight: 50.0000 chunk 110 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 497 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20350 Z= 0.199 Angle : 0.539 8.103 27778 Z= 0.270 Chirality : 0.043 0.403 3338 Planarity : 0.004 0.076 3550 Dihedral : 6.039 74.365 3284 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.05 % Favored : 92.72 % Rotamer: Outliers : 3.23 % Allowed : 29.78 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2666 helix: 1.94 (0.16), residues: 1078 sheet: -1.57 (0.34), residues: 262 loop : -1.87 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 636 HIS 0.003 0.001 HIS B 497 PHE 0.012 0.001 PHE C 533 TYR 0.020 0.001 TYR B 705 ARG 0.003 0.000 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 170 time to evaluate : 2.272 Fit side-chains REVERT: A 679 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5753 (t80) outliers start: 57 outliers final: 43 residues processed: 219 average time/residue: 0.2456 time to fit residues: 91.1017 Evaluate side-chains 210 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 50.0000 chunk 77 optimal weight: 0.0020 chunk 207 optimal weight: 0.0980 chunk 169 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 221 optimal weight: 0.0970 chunk 247 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 796 GLN B 171 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN D 171 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20350 Z= 0.130 Angle : 0.506 7.416 27778 Z= 0.251 Chirality : 0.042 0.413 3338 Planarity : 0.004 0.075 3550 Dihedral : 4.639 53.772 3281 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.34 % Favored : 93.47 % Rotamer: Outliers : 3.06 % Allowed : 30.29 % Favored : 66.65 % 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: -0.19 (0.17), residues: 2666 helix: 2.07 (0.16), residues: 1076 sheet: -1.54 (0.36), residues: 242 loop : -1.80 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 636 HIS 0.002 0.000 HIS C 94 PHE 0.015 0.001 PHE C 113 TYR 0.014 0.001 TYR D 705 ARG 0.006 0.000 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 179 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 679 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.5322 (t80) REVERT: B 773 CYS cc_start: 0.2842 (OUTLIER) cc_final: 0.2260 (m) REVERT: B 829 HIS cc_start: 0.7632 (m90) cc_final: 0.7409 (m90) REVERT: D 773 CYS cc_start: 0.2782 (OUTLIER) cc_final: 0.2184 (m) REVERT: D 784 PHE cc_start: 0.8023 (t80) cc_final: 0.7773 (t80) REVERT: D 829 HIS cc_start: 0.7624 (m90) cc_final: 0.7353 (m90) outliers start: 54 outliers final: 33 residues processed: 227 average time/residue: 0.2509 time to fit residues: 95.4815 Evaluate side-chains 204 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 0.0670 chunk 167 optimal weight: 30.0000 chunk 250 optimal weight: 0.9980 chunk 264 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20350 Z= 0.213 Angle : 0.525 7.374 27778 Z= 0.261 Chirality : 0.042 0.408 3338 Planarity : 0.004 0.073 3550 Dihedral : 4.356 53.823 3281 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.71 % Favored : 93.10 % Rotamer: Outliers : 4.42 % Allowed : 29.22 % Favored : 66.36 % 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: -0.16 (0.17), residues: 2666 helix: 2.11 (0.16), residues: 1080 sheet: -1.59 (0.34), residues: 262 loop : -1.79 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 636 HIS 0.004 0.001 HIS B 497 PHE 0.017 0.001 PHE A 113 TYR 0.021 0.001 TYR D 705 ARG 0.004 0.000 ARG D 821 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 172 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 679 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.5495 (t80) REVERT: C 340 PHE cc_start: 0.5809 (m-80) cc_final: 0.5529 (m-80) REVERT: C 427 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7813 (p0) outliers start: 78 outliers final: 61 residues processed: 244 average time/residue: 0.2501 time to fit residues: 102.9110 Evaluate side-chains 234 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 3 optimal weight: 40.0000 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 135 optimal weight: 0.9990 chunk 237 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20350 Z= 0.200 Angle : 0.527 8.801 27778 Z= 0.262 Chirality : 0.042 0.405 3338 Planarity : 0.004 0.076 3550 Dihedral : 4.330 53.851 3281 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 4.47 % Allowed : 29.78 % Favored : 65.74 % 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 (0.17), residues: 2666 helix: 2.11 (0.16), residues: 1080 sheet: -1.63 (0.34), residues: 262 loop : -1.79 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 636 HIS 0.003 0.001 HIS A 780 PHE 0.014 0.001 PHE A 113 TYR 0.024 0.001 TYR A 578 ARG 0.002 0.000 ARG D 821 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 175 time to evaluate : 2.149 Fit side-chains REVERT: A 577 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7504 (mp) REVERT: A 679 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.5461 (t80) REVERT: C 125 MET cc_start: 0.7466 (mmm) cc_final: 0.7057 (mtt) REVERT: C 340 PHE cc_start: 0.5752 (m-80) cc_final: 0.5480 (m-80) outliers start: 79 outliers final: 69 residues processed: 246 average time/residue: 0.2420 time to fit residues: 101.4051 Evaluate side-chains 243 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 172 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 10.0000 chunk 238 optimal weight: 20.0000 chunk 52 optimal weight: 0.3980 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 87 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN B 171 GLN B 497 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN D 171 GLN D 497 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 20350 Z= 0.530 Angle : 0.697 8.275 27778 Z= 0.358 Chirality : 0.047 0.378 3338 Planarity : 0.004 0.074 3550 Dihedral : 5.013 53.939 3281 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.45 % Favored : 90.36 % Rotamer: Outliers : 6.06 % Allowed : 29.28 % Favored : 64.67 % 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: -0.65 (0.17), residues: 2666 helix: 1.58 (0.16), residues: 1098 sheet: -1.99 (0.35), residues: 246 loop : -1.96 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 636 HIS 0.009 0.002 HIS A 780 PHE 0.029 0.003 PHE C 533 TYR 0.026 0.002 TYR C 578 ARG 0.003 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 172 time to evaluate : 2.185 Fit side-chains REVERT: A 477 HIS cc_start: 0.9033 (OUTLIER) cc_final: 0.8724 (p90) REVERT: C 155 MET cc_start: 0.8587 (tmm) cc_final: 0.8386 (ttt) REVERT: C 477 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8694 (p90) outliers start: 107 outliers final: 81 residues processed: 269 average time/residue: 0.2356 time to fit residues: 106.4635 Evaluate side-chains 250 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 167 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 50.0000 chunk 29 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 193 optimal weight: 50.0000 chunk 149 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 148 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 430 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 20350 Z= 0.583 Angle : 0.738 8.759 27778 Z= 0.377 Chirality : 0.048 0.373 3338 Planarity : 0.005 0.076 3550 Dihedral : 5.314 54.328 3281 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.24 % Favored : 89.65 % Rotamer: Outliers : 6.12 % Allowed : 29.67 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2666 helix: 1.29 (0.16), residues: 1098 sheet: -1.87 (0.37), residues: 220 loop : -2.27 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 636 HIS 0.008 0.002 HIS A 780 PHE 0.030 0.003 PHE A 533 TYR 0.025 0.002 TYR C 456 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 160 time to evaluate : 2.191 Fit side-chains REVERT: A 679 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6173 (t80) REVERT: C 125 MET cc_start: 0.7722 (mmm) cc_final: 0.7129 (mtp) REVERT: C 155 MET cc_start: 0.8537 (tmm) cc_final: 0.8330 (ttt) outliers start: 108 outliers final: 80 residues processed: 258 average time/residue: 0.2427 time to fit residues: 106.5061 Evaluate side-chains 240 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 159 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 827 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 0.1980 chunk 105 optimal weight: 0.3980 chunk 157 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 50.0000 chunk 167 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 207 optimal weight: 40.0000 chunk 240 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 497 HIS ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20350 Z= 0.162 Angle : 0.573 10.805 27778 Z= 0.280 Chirality : 0.043 0.392 3338 Planarity : 0.004 0.078 3550 Dihedral : 4.552 53.328 3277 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.13 % Favored : 92.76 % Rotamer: Outliers : 2.77 % Allowed : 32.79 % Favored : 64.44 % 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: -0.55 (0.17), residues: 2666 helix: 1.81 (0.16), residues: 1086 sheet: -2.01 (0.33), residues: 266 loop : -1.98 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 636 HIS 0.003 0.001 HIS B 513 PHE 0.015 0.001 PHE C 340 TYR 0.015 0.001 TYR C 578 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 2.435 Fit side-chains REVERT: A 679 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5413 (t80) REVERT: B 681 MET cc_start: 0.5297 (mmm) cc_final: 0.5058 (mmp) outliers start: 49 outliers final: 43 residues processed: 217 average time/residue: 0.2450 time to fit residues: 90.2917 Evaluate side-chains 216 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 172 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 636 TRP Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 827 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 232 optimal weight: 50.0000 chunk 245 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 497 HIS ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 686 GLN D 171 GLN D 497 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20350 Z= 0.245 Angle : 0.587 12.372 27778 Z= 0.287 Chirality : 0.043 0.394 3338 Planarity : 0.004 0.077 3550 Dihedral : 4.495 54.153 3277 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.29 % Favored : 91.60 % Rotamer: Outliers : 3.00 % Allowed : 32.62 % Favored : 64.38 % 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: -0.51 (0.17), residues: 2666 helix: 1.84 (0.16), residues: 1084 sheet: -1.96 (0.33), residues: 266 loop : -1.97 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP A 636 HIS 0.023 0.001 HIS B 497 PHE 0.015 0.001 PHE A 533 TYR 0.017 0.001 TYR B 705 ARG 0.002 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 173 time to evaluate : 2.335 Fit side-chains REVERT: A 679 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.5372 (t80) REVERT: B 681 MET cc_start: 0.5446 (mmm) cc_final: 0.5192 (mmp) outliers start: 53 outliers final: 50 residues processed: 220 average time/residue: 0.2534 time to fit residues: 94.3351 Evaluate side-chains 224 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 173 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 272 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 167 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20350 Z= 0.148 Angle : 0.566 12.357 27778 Z= 0.273 Chirality : 0.043 0.398 3338 Planarity : 0.004 0.077 3550 Dihedral : 4.294 53.750 3277 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 2.60 % Allowed : 32.96 % Favored : 64.44 % 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: -0.39 (0.17), residues: 2666 helix: 1.91 (0.16), residues: 1086 sheet: -1.82 (0.34), residues: 252 loop : -1.90 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP A 636 HIS 0.047 0.001 HIS D 497 PHE 0.019 0.001 PHE C 340 TYR 0.019 0.001 TYR D 673 ARG 0.002 0.000 ARG C 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 2.184 Fit side-chains REVERT: A 502 MET cc_start: 0.8784 (mmm) cc_final: 0.8301 (mmm) REVERT: A 679 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.4864 (t80) REVERT: B 681 MET cc_start: 0.5081 (mmm) cc_final: 0.4824 (mmp) REVERT: B 729 MET cc_start: 0.8366 (tpp) cc_final: 0.7992 (tpt) REVERT: C 155 MET cc_start: 0.8590 (tmm) cc_final: 0.8294 (ttt) REVERT: D 212 LEU cc_start: 0.7547 (pt) cc_final: 0.7310 (pp) REVERT: D 729 MET cc_start: 0.8364 (tpp) cc_final: 0.7981 (tpt) outliers start: 46 outliers final: 44 residues processed: 220 average time/residue: 0.2395 time to fit residues: 89.4268 Evaluate side-chains 222 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 177 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 223 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.163622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137456 restraints weight = 41927.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128479 restraints weight = 61173.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128050 restraints weight = 65481.122| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20350 Z= 0.187 Angle : 0.565 12.550 27778 Z= 0.273 Chirality : 0.042 0.394 3338 Planarity : 0.004 0.077 3550 Dihedral : 4.236 54.149 3277 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.58 % Favored : 92.31 % Rotamer: Outliers : 3.11 % Allowed : 32.84 % Favored : 64.04 % 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: -0.34 (0.17), residues: 2666 helix: 1.96 (0.17), residues: 1088 sheet: -1.82 (0.34), residues: 252 loop : -1.89 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP A 636 HIS 0.003 0.001 HIS A 780 PHE 0.016 0.001 PHE C 340 TYR 0.018 0.001 TYR D 705 ARG 0.002 0.000 ARG D 821 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3081.60 seconds wall clock time: 56 minutes 53.95 seconds (3413.95 seconds total)