Starting phenix.real_space_refine on Sun Mar 17 19:20:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu8_31309/03_2024/7eu8_31309_neut_updated.pdb" } resolution = 4.07 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 Cl 1 4.86 5 C 11880 2.51 5 N 3207 2.21 5 O 3527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 4607 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 31, 'TRANS': 729} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1452 Unresolved non-hydrogen angles: 1816 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 32, 'TYR:plan': 7, 'ASN:plan1': 28, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 43, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 802 Chain: "B" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 4546 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 355} Link IDs: {'PTRANS': 26, 'TRANS': 716} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1353 Unresolved non-hydrogen angles: 1690 Unresolved non-hydrogen dihedrals: 1135 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 32, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 22, 'GLU:plan': 38, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 788 Chain: "C" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 4844 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 323} Link IDs: {'PTRANS': 32, 'TRANS': 739} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1294 Unresolved non-hydrogen angles: 1603 Unresolved non-hydrogen dihedrals: 1075 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 31, 'TYR:plan': 8, 'ASN:plan1': 24, 'TRP:plan': 3, 'HIS:plan': 12, 'PHE:plan': 10, 'GLU:plan': 47, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 831 Chain: "D" Number of atoms: 4559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 4559 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 322} Link IDs: {'PTRANS': 26, 'TRANS': 707} Chain breaks: 7 Unresolved non-hydrogen bonds: 1274 Unresolved non-hydrogen angles: 1581 Unresolved non-hydrogen dihedrals: 1081 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 29, 'TYR:plan': 14, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 21, 'GLU:plan': 36, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 745 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'JC9': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.43, per 1000 atoms: 0.56 Number of scatterers: 18670 At special positions: 0 Unit cell: (129.256, 146.376, 181.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 55 16.00 O 3527 8.00 N 3207 7.00 C 11880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 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 NAG-ASN " NAG A 901 " - " ASN A 203 " " NAG B 901 " - " ASN B 688 " " NAG B 902 " - " ASN B 341 " " NAG C 901 " - " ASN C 203 " " NAG D 901 " - " ASN D 542 " " NAG D 902 " - " ASN D 688 " " NAG D 903 " - " ASN D 348 " Time building additional restraints: 7.43 Conformation dependent library (CDL) restraints added in 4.0 seconds 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5618 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 107 helices and 28 sheets defined 39.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.838A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.946A pdb=" N LYS A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 171 through 183 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.872A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 501 through 507 removed outlier: 3.837A pdb=" N LEU A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 581 removed outlier: 4.208A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.964A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 655 removed outlier: 3.657A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.536A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.509A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 784 through 792 Processing helix chain 'A' and resid 814 through 840 removed outlier: 3.957A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 56 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 106 through 119 Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 180 through 192 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 234 through 247 removed outlier: 3.943A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 311 Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.748A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 496 through 502 Processing helix chain 'B' and resid 517 through 522 removed outlier: 3.757A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 565 removed outlier: 3.578A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 575 Processing helix chain 'B' and resid 603 through 613 removed outlier: 4.518A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 655 removed outlier: 3.915A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 674 through 677 No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 690 through 698 Processing helix chain 'B' and resid 701 through 708 removed outlier: 3.513A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 773 through 785 removed outlier: 3.836A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 796 removed outlier: 3.788A pdb=" N TRP B 796 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 830 removed outlier: 3.786A pdb=" N GLY B 826 " --> pdb=" O TYR B 823 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 828 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 829 " --> pdb=" O GLY B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 835 No H-bonds generated for 'chain 'B' and resid 832 through 835' Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 127 through 130 No H-bonds generated for 'chain 'C' and resid 127 through 130' Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 205 through 214 removed outlier: 3.565A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 258 through 261 No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.973A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 459 through 470 Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 560 through 581 removed outlier: 3.648A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 614 removed outlier: 3.762A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 637 removed outlier: 3.542A pdb=" N ALA C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 655 Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 688 through 695 Processing helix chain 'C' and resid 700 through 706 removed outlier: 3.656A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET C 706 " --> pdb=" O MET C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 722 Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.525A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 781 Processing helix chain 'C' and resid 784 through 792 Processing helix chain 'C' and resid 810 through 840 removed outlier: 4.403A pdb=" N ALA C 814 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY C 815 " --> pdb=" O ASN C 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 51 No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 78 through 90 removed outlier: 3.520A pdb=" N MET D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 removed outlier: 3.524A pdb=" N ALA D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 164 Processing helix chain 'D' and resid 177 through 192 removed outlier: 4.454A pdb=" N GLN D 180 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASP D 181 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL D 183 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN D 192 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 222 Processing helix chain 'D' and resid 234 through 247 removed outlier: 4.079A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 311 Processing helix chain 'D' and resid 321 through 323 No H-bonds generated for 'chain 'D' and resid 321 through 323' Processing helix chain 'D' and resid 332 through 340 Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 517 through 522 removed outlier: 3.668A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 578 removed outlier: 4.392A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 629 through 655 removed outlier: 3.677A pdb=" N ILE D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 674 through 677 No H-bonds generated for 'chain 'D' and resid 674 through 677' Processing helix chain 'D' and resid 690 through 698 Processing helix chain 'D' and resid 700 through 709 removed outlier: 4.065A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE D 709 " --> pdb=" O TYR D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 743 through 745 No H-bonds generated for 'chain 'D' and resid 743 through 745' Processing helix chain 'D' and resid 773 through 785 Processing helix chain 'D' and resid 788 through 796 Processing helix chain 'D' and resid 815 through 836 removed outlier: 4.368A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.637A pdb=" N LEU A 138 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.889A pdb=" N VAL A 218 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N LEU A 166 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 220 " --> pdb=" O LEU A 166 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 267 through 271 Processing sheet with id= D, first strand: chain 'A' and resid 354 through 357 Processing sheet with id= E, first strand: chain 'A' and resid 397 through 401 removed outlier: 6.431A pdb=" N THR A 473 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 400 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU A 475 " --> pdb=" O ILE A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.862A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 486 through 488 removed outlier: 3.737A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.859A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 540 through 543 removed outlier: 3.650A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= K, first strand: chain 'B' and resid 227 through 229 removed outlier: 6.401A pdb=" N THR B 255 " --> pdb=" O ILE B 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 278 through 282 Processing sheet with id= M, first strand: chain 'B' and resid 475 through 480 removed outlier: 7.773A pdb=" N MET B 508 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 434 through 437 Processing sheet with id= O, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.511A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 762 " --> pdb=" O ILE B 530 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 534 through 537 removed outlier: 3.744A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 537 " --> pdb=" O PHE B 729 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE B 729 " --> pdb=" O MET B 537 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 91 through 93 removed outlier: 7.817A pdb=" N LEU C 119 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 138 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.629A pdb=" N VAL C 218 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU C 166 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE C 220 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 267 through 270 Processing sheet with id= T, first strand: chain 'C' and resid 354 through 357 Processing sheet with id= U, first strand: chain 'C' and resid 397 through 401 removed outlier: 6.664A pdb=" N THR C 473 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE C 400 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'C' and resid 435 through 437 Processing sheet with id= W, first strand: chain 'C' and resid 534 through 537 removed outlier: 3.959A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER C 756 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 728 through 730 Processing sheet with id= Y, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.868A pdb=" N VAL D 39 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 98 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 278 through 282 Processing sheet with id= AA, first strand: chain 'D' and resid 378 through 380 removed outlier: 4.017A pdb=" N LYS D 378 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN D 385 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS D 380 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 478 through 480 removed outlier: 5.910A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET D 508 " --> pdb=" O VAL D 409 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB 774 hydrogen bonds defined for protein. 2115 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: 6.19 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6288 1.34 - 1.46: 4439 1.46 - 1.58: 8207 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 19011 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C GLN C 556 " pdb=" N PRO C 557 " ideal model delta sigma weight residual 1.335 1.385 -0.050 1.28e-02 6.10e+03 1.55e+01 bond pdb=" C ALA D 414 " pdb=" N PRO D 415 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.25e-02 6.40e+03 1.38e+01 bond pdb=" C ALA B 414 " pdb=" N PRO B 415 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.25e-02 6.40e+03 1.35e+01 bond pdb=" C8 JC9 B 903 " pdb="CL1 JC9 B 903 " ideal model delta sigma weight residual 1.785 1.726 0.059 2.00e-02 2.50e+03 8.85e+00 ... (remaining 19006 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.37: 619 107.37 - 114.03: 11043 114.03 - 120.68: 7574 120.68 - 127.34: 6860 127.34 - 133.99: 209 Bond angle restraints: 26305 Sorted by residual: angle pdb=" C HIS D 325 " pdb=" CA HIS D 325 " pdb=" CB HIS D 325 " ideal model delta sigma weight residual 116.34 110.42 5.92 1.40e+00 5.10e-01 1.79e+01 angle pdb=" CA LEU C 541 " pdb=" CB LEU C 541 " pdb=" CG LEU C 541 " ideal model delta sigma weight residual 116.30 126.56 -10.26 3.50e+00 8.16e-02 8.59e+00 angle pdb=" CA GLN C 556 " pdb=" C GLN C 556 " pdb=" N PRO C 557 " ideal model delta sigma weight residual 118.44 122.83 -4.39 1.59e+00 3.96e-01 7.61e+00 angle pdb=" CA GLN A 556 " pdb=" C GLN A 556 " pdb=" N PRO A 557 " ideal model delta sigma weight residual 118.44 122.72 -4.28 1.59e+00 3.96e-01 7.23e+00 angle pdb=" CA ALA D 414 " pdb=" C ALA D 414 " pdb=" N PRO D 415 " ideal model delta sigma weight residual 118.44 122.67 -4.23 1.59e+00 3.96e-01 7.08e+00 ... (remaining 26300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 10777 23.48 - 46.95: 152 46.95 - 70.43: 14 70.43 - 93.91: 0 93.91 - 117.39: 9 Dihedral angle restraints: 10952 sinusoidal: 2291 harmonic: 8661 Sorted by residual: dihedral pdb=" CA ALA B 414 " pdb=" C ALA B 414 " pdb=" N PRO B 415 " pdb=" CA PRO B 415 " ideal model delta harmonic sigma weight residual 180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ALA D 414 " pdb=" C ALA D 414 " pdb=" N PRO D 415 " pdb=" CA PRO D 415 " ideal model delta harmonic sigma weight residual -180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 54.43 -117.39 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 10949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.069: 3371 1.069 - 2.139: 0 2.139 - 3.208: 0 3.208 - 4.277: 0 4.277 - 5.347: 1 Chirality restraints: 3372 Sorted by residual: chirality pdb=" C1 JC9 B 903 " pdb=" C2 JC9 B 903 " pdb=" C5 JC9 B 903 " pdb=" C7 JC9 B 903 " both_signs ideal model delta sigma weight residual False 2.73 -2.61 5.35 2.00e-01 2.50e+01 7.15e+02 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 203 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 348 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 3369 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 556 " -0.048 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO A 557 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 414 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 415 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 415 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 415 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 414 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO D 415 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " 0.037 5.00e-02 4.00e+02 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1740 2.74 - 3.28: 18639 3.28 - 3.82: 30970 3.82 - 4.36: 28897 4.36 - 4.90: 53063 Nonbonded interactions: 133309 Sorted by model distance: nonbonded pdb=" O ALA D 794 " pdb=" OG1 THR D 798 " model vdw 2.206 2.440 nonbonded pdb=" O LEU A 672 " pdb=" OH TYR A 681 " model vdw 2.232 2.440 nonbonded pdb=" O ARG C 671 " pdb=" OH TYR C 681 " model vdw 2.262 2.440 nonbonded pdb=" N GLY A 250 " pdb=" OE2 GLU A 253 " model vdw 2.266 2.520 nonbonded pdb=" OG SER C 126 " pdb=" OG SER C 129 " model vdw 2.293 2.440 ... (remaining 133304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 81 or (resid 82 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 108 or (resid 109 throu \ gh 111 and (name N or name CA or name C or name O or name CB )) or resid 112 thr \ ough 186 or (resid 189 through 198 and (name N or name CA or name C or name O or \ name CB )) or resid 199 through 244 or (resid 245 through 246 and (name N or na \ me CA or name C or name O or name CB )) or resid 247 through 252 or (resid 253 t \ hrough 255 and (name N or name CA or name C or name O or name CB )) or resid 256 \ through 269 or (resid 270 through 273 and (name N or name CA or name C or name \ O or name CB )) or resid 274 through 370 or (resid 371 through 381 and (name N o \ r name CA or name C or name O or name CB )) or resid 382 through 433 or (resid 4 \ 34 through 435 and (name N or name CA or name C or name O or name CB )) or resid \ 436 through 449 or (resid 450 and (name N or name CA or name C or name O or nam \ e CB )) or resid 451 through 486 or (resid 487 through 497 and (name N or name C \ A or name C or name O or name CB )) or resid 498 through 503 or (resid 504 throu \ gh 507 and (name N or name CA or name C or name O or name CB )) or resid 508 thr \ ough 511 or (resid 512 and (name N or name CA or name C or name O or name CB )) \ or resid 513 through 518 or (resid 519 and (name N or name CA or name C or name \ O or name CB )) or resid 520 through 562 or (resid 563 through 564 and (name N o \ r name CA or name C or name O or name CB )) or resid 565 through 570 or (resid 5 \ 71 through 572 and (name N or name CA or name C or name O or name CB )) or resid \ 573 through 618 or (resid 626 through 627 and (name N or name CA or name C or n \ ame O or name CB )) or resid 628 through 630 or (resid 631 through 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 or (resid 634 and ( \ name N or name CA or name C or name O or name CB )) or resid 635 through 663 or \ (resid 664 and (name N or name CA or name C or name O or name CB )) or resid 665 \ through 666 or (resid 667 through 668 and (name N or name CA or name C or name \ O or name CB )) or resid 669 through 671 or (resid 672 through 674 and (name N o \ r name CA or name C or name O or name CB )) or resid 675 through 695 or (resid 6 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 697 through \ 706 or (resid 707 through 708 and (name N or name CA or name C or name O or nam \ e CB )) or resid 709 through 737 or (resid 738 through 740 and (name N or name C \ A or name C or name O or name CB )) or resid 741 through 762 or (resid 763 throu \ gh 766 and (name N or name CA or name C or name O or name CB )) or resid 767 thr \ ough 790 or (resid 791 and (name N or name CA or name C or name O or name CB )) \ or resid 792 through 809 or (resid 810 through 814 and (name N or name CA or nam \ e C or name O or name CB )) or resid 815 through 818 or (resid 819 and (name N o \ r name CA or name C or name O or name CB )) or resid 820 through 841 or resid 90 \ 1)) selection = (chain 'C' and (resid 28 through 32 or (resid 33 through 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 63 or (resid 64 through \ 66 and (name N or name CA or name C or name O or name CB )) or resid 67 through \ 68 or (resid 69 through 77 and (name N or name CA or name C or name O or name C \ B )) or resid 78 or (resid 79 through 92 and (name N or name CA or name C or nam \ e O or name CB )) or resid 93 through 97 or (resid 98 through 103 and (name N or \ name CA or name C or name O or name CB )) or resid 104 through 106 or (resid 10 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 108 through \ 109 or (resid 110 through 111 and (name N or name CA or name C or name O or name \ CB )) or resid 112 through 118 or (resid 119 and (name N or name CA or name C o \ r name O or name CB )) or resid 120 or (resid 121 through 122 and (name N or nam \ e CA or name C or name O or name CB )) or resid 123 through 124 or (resid 125 th \ rough 127 and (name N or name CA or name C or name O or name CB )) or resid 128 \ or (resid 129 through 131 and (name N or name CA or name C or name O or name CB \ )) or resid 132 or (resid 133 and (name N or name CA or name C or name O or name \ CB )) or resid 134 or (resid 135 through 137 and (name N or name CA or name C o \ r name O or name CB )) or resid 138 through 139 or (resid 140 and (name N or nam \ e CA or name C or name O or name CB )) or resid 141 through 146 or (resid 147 an \ d (name N or name CA or name C or name O or name CB )) or resid 148 or (resid 14 \ 9 through 150 and (name N or name CA or name C or name O or name CB )) or resid \ 151 or (resid 152 through 157 and (name N or name CA or name C or name O or name \ CB )) or resid 158 or (resid 159 and (name N or name CA or name C or name O or \ name CB )) or resid 160 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 or (resid 165 through 172 and (name N or \ name CA or name C or name O or name CB )) or resid 173 through 181 or (resid 18 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 183 or (resi \ d 184 through 198 and (name N or name CA or name C or name O or name CB )) or re \ sid 199 through 203 or (resid 204 and (name N or name CA or name C or name O or \ name CB )) or resid 205 through 220 or (resid 221 through 229 and (name N or nam \ e CA or name C or name O or name CB )) or resid 230 through 237 or (resid 238 th \ rough 241 and (name N or name CA or name C or name O or name CB )) or resid 242 \ or (resid 243 and (name N or name CA or name C or name O or name CB )) or (resid \ 244 through 246 and (name N or name CA or name C or name O or name CB )) or res \ id 247 or (resid 248 through 249 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 250 through 255 and (name N or name CA or name C or name O o \ r name CB )) or (resid 256 through 260 and (name N or name CA or name C or name \ O or name CB )) or resid 261 through 266 or (resid 267 and (name N or name CA or \ name C or name O or name CB )) or resid 268 through 271 or (resid 272 through 2 \ 73 and (name N or name CA or name C or name O or name CB )) or (resid 274 throug \ h 279 and (name N or name CA or name C or name O or name CB )) or resid 280 thro \ ugh 281 or (resid 282 through 285 and (name N or name CA or name C or name O or \ name CB )) or (resid 286 through 303 and (name N or name CA or name C or name O \ or name CB )) or resid 304 through 311 or (resid 312 through 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 318 or (resid 319 \ through 320 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 21 through 324 or (resid 325 through 326 and (name N or name CA or name C or nam \ e O or name CB )) or resid 327 or (resid 328 through 332 and (name N or name CA \ or name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (na \ me N or name CA or name C or name O or name CB )) or resid 336 through 339 or (r \ esid 340 through 343 and (name N or name CA or name C or name O or name CB )) or \ (resid 344 through 351 and (name N or name CA or name C or name O or name CB )) \ or resid 352 or (resid 353 through 364 and (name N or name CA or name C or name \ O or name CB )) or resid 365 through 372 or (resid 373 through 381 and (name N \ or name CA or name C or name O or name CB )) or resid 382 through 396 or (resid \ 397 and (name N or name CA or name C or name O or name CB )) or resid 398 throug \ h 410 or (resid 411 through 412 and (name N or name CA or name C or name O or na \ me CB )) or resid 413 or (resid 414 through 417 and (name N or name CA or name C \ or name O or name CB )) or resid 418 through 424 or (resid 425 through 427 and \ (name N or name CA or name C or name O or name CB )) or resid 428 through 430 or \ (resid 431 through 435 and (name N or name CA or name C or name O or name CB )) \ or resid 436 through 442 or (resid 443 through 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 or (resid 446 through 450 and (name N \ or name CA or name C or name O or name CB )) or resid 451 through 458 or (resid \ 459 through 471 and (name N or name CA or name C or name O or name CB )) or resi \ d 472 or (resid 473 and (name N or name CA or name C or name O or name CB )) or \ resid 474 through 475 or (resid 476 and (name N or name CA or name C or name O o \ r name CB )) or resid 477 or (resid 478 through 481 and (name N or name CA or na \ me C or name O or name CB )) or resid 482 through 485 or (resid 486 through 497 \ and (name N or name CA or name C or name O or name CB )) or resid 498 or (resid \ 499 and (name N or name CA or name C or name O or name CB )) or resid 500 throug \ h 501 or (resid 502 and (name N or name CA or name C or name O or name CB )) or \ (resid 503 through 507 and (name N or name CA or name C or name O or name CB )) \ or resid 508 through 517 or (resid 518 through 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 or (resid 521 through 522 and (name N o \ r name CA or name C or name O or name CB )) or resid 523 through 538 or (resid 5 \ 39 through 545 and (name N or name CA or name C or name O or name CB )) or (resi \ d 552 through 556 and (name N or name CA or name C or name O or name CB )) or re \ sid 557 through 559 or (resid 560 and (name N or name CA or name C or name O or \ name CB )) or resid 561 through 563 or (resid 564 and (name N or name CA or name \ C or name O or name CB )) or resid 565 through 577 or (resid 578 through 603 an \ d (name N or name CA or name C or name O or name CB )) or resid 604 through 609 \ or (resid 610 and (name N or name CA or name C or name O or name CB )) or resid \ 611 through 618 or resid 626 through 670 or (resid 671 through 674 and (name N o \ r name CA or name C or name O or name CB )) or resid 675 through 729 or (resid 7 \ 30 through 732 and (name N or name CA or name C or name O or name CB )) or resid \ 733 through 770 or (resid 771 and (name N or name CA or name C or name O or nam \ e CB )) or resid 772 through 784 or (resid 785 through 787 and (name N or name C \ A or name C or name O or name CB )) or resid 788 through 807 or (resid 808 and ( \ name N or name CA or name C or name O or name CB )) or resid 809 through 841 or \ resid 901)) } ncs_group { reference = (chain 'B' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 57 or (resid 58 through 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 69 or (resid 70 and (name N or na \ me CA or name C or name O or name CB )) or resid 71 through 84 or (resid 85 thro \ ugh 89 and (name N or name CA or name C or name O or name CB )) or resid 90 thro \ ugh 107 or (resid 108 through 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or (resid 125 through 127 and (name N or name CA or n \ ame C or name O or name CB )) or resid 128 through 145 or (resid 146 and (name N \ or name CA or name C or name O or name CB )) or resid 147 through 148 or (resid \ 149 through 155 and (name N or name CA or name C or name O or name CB )) or res \ id 156 through 159 or (resid 160 and (name N or name CA or name C or name O or n \ ame CB )) or resid 161 through 165 or (resid 166 and (name N or name CA or name \ C or name O or name CB )) or resid 167 through 173 or (resid 174 through 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 200 o \ r resid 215 through 237 or (resid 238 through 239 and (name N or name CA or name \ C or name O or name CB )) or resid 240 or (resid 241 through 242 and (name N or \ name CA or name C or name O or name CB )) or resid 243 through 244 or (resid 24 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 246 through \ 248 or resid 253 through 261 or (resid 262 through 263 and (name N or name CA or \ name C or name O or name CB )) or (resid 264 through 269 and (name N or name CA \ or name C or name O or name CB )) or resid 270 through 277 or (resid 278 and (n \ ame N or name CA or name C or name O or name CB )) or resid 279 through 296 or ( \ resid 297 through 300 and (name N or name CA or name C or name O or name CB )) o \ r resid 301 through 305 or (resid 306 through 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 310 or (resid 311 through 314 an \ d (name N or name CA or name C or name O or name CB )) or resid 315 through 349 \ or (resid 350 and (name N or name CA or name C or name O or name CB )) or resid \ 351 through 358 or (resid 359 and (name N or name CA or name C or name O or name \ CB )) or resid 360 through 362 or (resid 363 through 366 and (name N or name CA \ or name C or name O or name CB )) or resid 367 through 392 or (resid 406 and (n \ ame N or name CA or name C or name O or name CB )) or resid 407 through 422 or ( \ resid 423 and (name N or name CA or name C or name O or name CB )) or resid 424 \ through 431 or (resid 432 through 433 and (name N or name CA or name C or name O \ or name CB )) or resid 434 through 438 or resid 451 or (resid 452 through 455 a \ nd (name N or name CA or name C or name O or name CB )) or resid 456 through 474 \ or (resid 475 and (name N or name CA or name C or name O or name CB )) or resid \ 476 through 479 or (resid 480 and (name N or name CA or name C or name O or nam \ e CB )) or resid 481 through 499 or (resid 500 and (name N or name CA or name C \ or name O or name CB )) or resid 501 through 507 or (resid 508 through 509 and ( \ name N or name CA or name C or name O or name CB )) or resid 510 through 518 or \ (resid 519 and (name N or name CA or name C or name O or name CB )) or resid 520 \ through 524 or (resid 525 and (name N or name CA or name C or name O or name CB \ )) or resid 526 through 544 or (resid 545 and (name N or name CA or name C or n \ ame O or name CB )) or resid 546 through 554 or (resid 555 through 556 and (name \ N or name CA or name C or name O or name CB )) or resid 557 through 566 or (res \ id 567 through 568 and (name N or name CA or name C or name O or name CB )) or r \ esid 569 or (resid 570 through 571 and (name N or name CA or name C or name O or \ name CB )) or resid 572 through 573 or (resid 574 through 575 and (name N or na \ me CA or name C or name O or name CB )) or resid 576 through 601 or (resid 602 a \ nd (name N or name CA or name C or name O or name CB )) or resid 603 through 613 \ or (resid 614 through 615 and (name N or name CA or name C or name O or name CB \ )) or resid 616 or (resid 617 through 618 and (name N or name CA or name C or n \ ame O or name CB )) or resid 619 through 629 or (resid 630 through 631 and (name \ N or name CA or name C or name O or name CB )) or resid 632 through 637 or (res \ id 638 through 639 and (name N or name CA or name C or name O or name CB )) or r \ esid 640 through 642 or (resid 643 through 644 and (name N or name CA or name C \ or name O or name CB )) or resid 645 through 696 or (resid 697 through 698 and ( \ name N or name CA or name C or name O or name CB )) or resid 699 through 704 or \ (resid 705 through 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 768 or (resid 769 and (name N or name CA or name C or name \ O or name CB )) or resid 770 through 772 or (resid 773 through 775 and (name N o \ r name CA or name C or name O or name CB )) or resid 776 through 788 or (resid 7 \ 89 through 791 and (name N or name CA or name C or name O or name CB )) or resid \ 792 through 815 or (resid 816 through 819 and (name N or name CA or name C or n \ ame O or name CB )) or resid 820 through 830 or (resid 831 and (name N or name C \ A or name C or name O or name CB )) or resid 832 through 837 or resid 901 throug \ h 902)) selection = (chain 'D' and (resid 34 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 40 or (resid 41 and (na \ me N or name CA or name C or name O or name CB )) or resid 42 through 45 or (res \ id 46 through 51 and (name N or name CA or name C or name O or name CB )) or res \ id 52 through 53 or (resid 54 through 65 and (name N or name CA or name C or nam \ e O or name CB )) or resid 66 through 75 or (resid 76 through 77 and (name N or \ name CA or name C or name O or name CB )) or resid 78 through 79 or (resid 80 an \ d (name N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 \ through 89 and (name N or name CA or name C or name O or name CB )) or resid 90 \ or (resid 91 through 95 and (name N or name CA or name C or name O or name CB )) \ or resid 96 through 102 or (resid 103 through 110 and (name N or name CA or nam \ e C or name O or name CB )) or resid 111 through 113 or (resid 114 and (name N o \ r name CA or name C or name O or name CB )) or resid 115 through 117 or (resid 1 \ 18 through 120 and (name N or name CA or name C or name O or name CB )) or resid \ 121 through 125 or (resid 126 through 127 and (name N or name CA or name C or n \ ame O or name CB )) or resid 128 through 130 or (resid 131 through 142 and (name \ N or name CA or name C or name O or name CB )) or resid 143 through 149 or (res \ id 150 through 155 and (name N or name CA or name C or name O or name CB )) or r \ esid 156 through 174 or (resid 175 through 176 and (name N or name CA or name C \ or name O or name CB )) or resid 177 through 180 or (resid 181 through 182 and ( \ name N or name CA or name C or name O or name CB )) or resid 183 through 185 or \ (resid 186 through 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 through 190 or (resid 191 through 192 and (name N or name CA or nam \ e C or name O or name CB )) or resid 193 through 198 or (resid 199 through 215 a \ nd (name N or name CA or name C or name O or name CB )) or resid 216 through 217 \ or (resid 218 through 224 and (name N or name CA or name C or name O or name CB \ )) or resid 225 through 227 or (resid 228 and (name N or name CA or name C or n \ ame O or name CB )) or resid 229 or (resid 230 and (name N or name CA or name C \ or name O or name CB )) or resid 231 or (resid 232 through 239 and (name N or na \ me CA or name C or name O or name CB )) or resid 240 through 255 or (resid 256 a \ nd (name N or name CA or name C or name O or name CB )) or resid 257 through 259 \ or (resid 260 through 263 and (name N or name CA or name C or name O or name CB \ )) or (resid 264 through 269 and (name N or name CA or name C or name O or name \ CB )) or resid 270 through 274 or (resid 275 and (name N or name CA or name C o \ r name O or name CB )) or resid 276 through 279 or (resid 280 through 287 and (n \ ame N or name CA or name C or name O or name CB )) or resid 288 through 292 or ( \ resid 293 through 295 and (name N or name CA or name C or name O or name CB )) o \ r (resid 296 through 300 and (name N or name CA or name C or name O or name CB ) \ ) or resid 301 through 311 or (resid 312 through 314 and (name N or name CA or n \ ame C or name O or name CB )) or resid 315 through 320 or (resid 321 through 327 \ and (name N or name CA or name C or name O or name CB )) or (resid 331 through \ 334 and (name N or name CA or name C or name O or name CB )) or resid 335 throug \ h 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) or \ (resid 340 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2)) or resid 341 through 347 or (resid 348 through 350 and (name N or nam \ e CA or name C or name O or name CB )) or resid 351 through 353 or (resid 354 an \ d (name N or name CA or name C or name O or name CB )) or resid 355 or (resid 35 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 357 through \ 361 or (resid 362 through 366 and (name N or name CA or name C or name O or name \ CB )) or (resid 367 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD2)) or (resid 368 through 372 and (name N or name CA or name C o \ r name O or name CB )) or resid 373 through 385 or (resid 386 through 387 and (n \ ame N or name CA or name C or name O or name CB )) or resid 388 through 389 or ( \ resid 390 and (name N or name CA or name C or name O or name CB )) or resid 391 \ or (resid 392 through 406 and (name N or name CA or name C or name O or name CB \ )) or resid 407 through 420 or (resid 421 and (name N or name CA or name C or na \ me O or name CB )) or resid 422 through 462 or (resid 463 and (name N or name CA \ or name C or name O or name CB )) or resid 464 through 478 or (resid 479 throug \ h 480 and (name N or name CA or name C or name O or name CB )) or resid 481 thro \ ugh 492 or (resid 493 and (name N or name CA or name C or name O or name CB )) o \ r resid 494 or (resid 495 and (name N or name CA or name C or name O or name CB \ )) or (resid 496 through 498 and (name N or name CA or name C or name O or name \ CB )) or resid 499 through 501 or (resid 502 through 506 and (name N or name CA \ or name C or name O or name CB )) or resid 507 through 511 or (resid 512 and (na \ me N or name CA or name C or name O or name CB )) or resid 513 or (resid 514 and \ (name N or name CA or name C or name O or name CB )) or resid 515 or (resid 516 \ through 519 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 20 through 521 or (resid 522 and (name N or name CA or name C or name O or name \ CB )) or resid 523 through 529 or (resid 530 through 531 and (name N or name CA \ or name C or name O or name CB )) or (resid 532 and (name N or name CA or name C \ or name O or name CB or name OG1)) or resid 533 through 537 or (resid 538 throu \ gh 540 and (name N or name CA or name C or name O or name CB )) or resid 541 thr \ ough 547 or (resid 548 through 549 and (name N or name CA or name C or name O or \ name CB )) or resid 550 through 600 or (resid 601 through 602 and (name N or na \ me CA or name C or name O or name CB )) or resid 603 through 607 or (resid 608 t \ hrough 609 and (name N or name CA or name C or name O or name CB )) or resid 610 \ through 614 or (resid 615 and (name N or name CA or name C or name O or name CB \ )) or resid 616 through 652 or (resid 653 through 654 and (name N or name CA or \ name C or name O or name CB )) or resid 655 through 662 or (resid 663 through 6 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 665 through \ 670 or (resid 671 through 673 and (name N or name CA or name C or name O or nam \ e CB )) or resid 674 through 708 or (resid 709 through 712 and (name N or name C \ A or name C or name O or name CB )) or resid 713 through 725 or (resid 726 throu \ gh 728 and (name N or name CA or name C or name O or name CB )) or resid 729 thr \ ough 756 or (resid 757 through 758 and (name N or name CA or name C or name O or \ name CB )) or resid 759 through 781 or (resid 782 and (name N or name CA or nam \ e C or name O or name CB )) or resid 783 through 790 or (resid 791 and (name N o \ r name CA or name C or name O or name CB )) or resid 792 or (resid 793 through 7 \ 94 and (name N or name CA or name C or name O or name CB )) or resid 795 through \ 803 or (resid 810 through 819 and (name N or name CA or name C or name O or nam \ e CB )) or resid 820 through 837 or resid 901 through 902)) } 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: 2.070 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: 6.870 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 51.980 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 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 : 0.002 0.089 19011 Z= 0.146 Angle : 0.421 10.258 26305 Z= 0.213 Chirality : 0.101 5.347 3372 Planarity : 0.003 0.071 3431 Dihedral : 8.954 117.386 5316 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.00 % Favored : 97.86 % Rotamer: Outliers : 3.51 % Allowed : 8.87 % Favored : 87.62 % 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: 1.10 (0.16), residues: 2948 helix: 2.76 (0.15), residues: 1209 sheet: -0.18 (0.35), residues: 239 loop : -0.88 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP D 635 HIS 0.002 0.000 HIS D 54 PHE 0.005 0.001 PHE B 550 TYR 0.009 0.000 TYR C 578 ARG 0.002 0.000 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 289 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 ASN cc_start: 0.8141 (t0) cc_final: 0.7914 (t0) REVERT: A 738 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.4772 (t80) REVERT: B 358 MET cc_start: 0.6008 (ttt) cc_final: 0.5637 (ttm) REVERT: C 636 TRP cc_start: 0.6439 (OUTLIER) cc_final: 0.6227 (t60) REVERT: D 181 ASP cc_start: 0.7460 (p0) cc_final: 0.6898 (p0) outliers start: 42 outliers final: 21 residues processed: 327 average time/residue: 0.2200 time to fit residues: 122.8746 Evaluate side-chains 213 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 153 optimal weight: 30.0000 chunk 121 optimal weight: 0.0370 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN C 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 19011 Z= 0.318 Angle : 0.676 29.275 26305 Z= 0.339 Chirality : 0.059 2.155 3372 Planarity : 0.005 0.066 3431 Dihedral : 5.816 113.362 3208 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.28 % Rotamer: Outliers : 0.33 % Allowed : 4.60 % Favored : 95.06 % 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 (0.16), residues: 2948 helix: 2.04 (0.15), residues: 1215 sheet: -0.72 (0.32), residues: 263 loop : -0.98 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 494 HIS 0.012 0.002 HIS A 780 PHE 0.022 0.003 PHE D 460 TYR 0.037 0.002 TYR B 731 ARG 0.004 0.001 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 2.112 Fit side-chains REVERT: A 650 ASN cc_start: 0.8244 (t0) cc_final: 0.8038 (t0) REVERT: D 181 ASP cc_start: 0.7956 (p0) cc_final: 0.7629 (p0) outliers start: 4 outliers final: 2 residues processed: 223 average time/residue: 0.2134 time to fit residues: 83.9184 Evaluate side-chains 185 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 294 optimal weight: 0.0030 chunk 243 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 93 optimal weight: 50.0000 chunk 218 optimal weight: 5.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19011 Z= 0.278 Angle : 0.654 24.569 26305 Z= 0.325 Chirality : 0.062 2.469 3372 Planarity : 0.004 0.067 3431 Dihedral : 5.222 91.181 3208 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 0.59 % Allowed : 6.95 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2948 helix: 1.61 (0.15), residues: 1220 sheet: -1.36 (0.30), residues: 278 loop : -1.19 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 247 HIS 0.009 0.001 HIS C 780 PHE 0.030 0.002 PHE D 529 TYR 0.035 0.002 TYR D 731 ARG 0.003 0.001 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 2.337 Fit side-chains REVERT: B 358 MET cc_start: 0.4200 (ttt) cc_final: 0.3215 (ttm) REVERT: C 502 MET cc_start: 0.7501 (mmm) cc_final: 0.7216 (mmm) REVERT: D 126 ILE cc_start: 0.6768 (mp) cc_final: 0.6326 (mm) REVERT: D 181 ASP cc_start: 0.7971 (p0) cc_final: 0.7683 (p0) REVERT: D 462 ILE cc_start: 0.8538 (mm) cc_final: 0.8254 (mm) outliers start: 7 outliers final: 1 residues processed: 211 average time/residue: 0.2065 time to fit residues: 78.0279 Evaluate side-chains 165 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 40.0000 chunk 130 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 289 optimal weight: 20.0000 chunk 143 optimal weight: 0.3980 chunk 259 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN B 311 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN D 649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19011 Z= 0.226 Angle : 0.589 25.464 26305 Z= 0.290 Chirality : 0.060 2.420 3372 Planarity : 0.004 0.069 3431 Dihedral : 4.845 91.938 3208 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.95 % Rotamer: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2948 helix: 1.69 (0.15), residues: 1211 sheet: -1.44 (0.31), residues: 272 loop : -1.21 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 247 HIS 0.006 0.001 HIS C 780 PHE 0.019 0.002 PHE D 529 TYR 0.016 0.002 TYR D 731 ARG 0.002 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 2.008 Fit side-chains REVERT: D 126 ILE cc_start: 0.6912 (mp) cc_final: 0.6469 (mm) REVERT: D 181 ASP cc_start: 0.8034 (p0) cc_final: 0.7811 (p0) outliers start: 2 outliers final: 0 residues processed: 197 average time/residue: 0.2126 time to fit residues: 74.9992 Evaluate side-chains 159 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 148 optimal weight: 4.9990 chunk 260 optimal weight: 0.0370 chunk 73 optimal weight: 6.9990 overall best weight: 4.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 HIS C 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19011 Z= 0.308 Angle : 0.647 24.965 26305 Z= 0.328 Chirality : 0.061 2.415 3372 Planarity : 0.004 0.069 3431 Dihedral : 5.179 80.139 3208 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % 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: -0.41 (0.16), residues: 2948 helix: 1.37 (0.15), residues: 1207 sheet: -1.80 (0.30), residues: 261 loop : -1.42 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 247 HIS 0.010 0.002 HIS C 780 PHE 0.024 0.002 PHE D 529 TYR 0.046 0.002 TYR D 388 ARG 0.004 0.001 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.159 Fit side-chains REVERT: D 126 ILE cc_start: 0.7148 (mp) cc_final: 0.6751 (mm) REVERT: D 181 ASP cc_start: 0.8055 (p0) cc_final: 0.7087 (t0) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.1985 time to fit residues: 68.8989 Evaluate side-chains 156 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 290 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN C 709 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19011 Z= 0.264 Angle : 0.610 24.749 26305 Z= 0.305 Chirality : 0.061 2.406 3372 Planarity : 0.004 0.072 3431 Dihedral : 4.986 75.066 3208 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.90 % Favored : 93.93 % Rotamer: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.65 % 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: -0.46 (0.16), residues: 2948 helix: 1.39 (0.15), residues: 1202 sheet: -1.91 (0.29), residues: 259 loop : -1.48 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 247 HIS 0.006 0.001 HIS A 709 PHE 0.022 0.002 PHE D 784 TYR 0.020 0.002 TYR D 731 ARG 0.002 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.286 Fit side-chains REVERT: B 358 MET cc_start: 0.5380 (ttm) cc_final: 0.4247 (ttm) REVERT: C 760 ILE cc_start: 0.9034 (mm) cc_final: 0.8567 (pt) REVERT: D 181 ASP cc_start: 0.8082 (p0) cc_final: 0.7152 (t0) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.2083 time to fit residues: 69.8274 Evaluate side-chains 154 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN C 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19011 Z= 0.346 Angle : 0.674 24.969 26305 Z= 0.346 Chirality : 0.062 2.372 3372 Planarity : 0.005 0.072 3431 Dihedral : 5.429 68.012 3208 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.23 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2948 helix: 1.06 (0.15), residues: 1211 sheet: -2.27 (0.28), residues: 276 loop : -1.73 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 247 HIS 0.006 0.002 HIS C 780 PHE 0.022 0.003 PHE B 144 TYR 0.051 0.002 TYR B 731 ARG 0.004 0.001 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.202 Fit side-chains revert: symmetry clash REVERT: B 358 MET cc_start: 0.5385 (ttm) cc_final: 0.4286 (ttm) REVERT: B 762 TYR cc_start: 0.8192 (p90) cc_final: 0.7950 (p90) REVERT: D 181 ASP cc_start: 0.8051 (p0) cc_final: 0.7125 (t0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2074 time to fit residues: 67.2650 Evaluate side-chains 153 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 172 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 50.0000 chunk 227 optimal weight: 4.9990 chunk 263 optimal weight: 0.0020 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19011 Z= 0.179 Angle : 0.574 24.474 26305 Z= 0.283 Chirality : 0.060 2.380 3372 Planarity : 0.004 0.073 3431 Dihedral : 4.789 63.558 3208 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.05 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2948 helix: 1.47 (0.15), residues: 1202 sheet: -1.97 (0.29), residues: 259 loop : -1.59 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 772 HIS 0.003 0.001 HIS A 134 PHE 0.020 0.001 PHE C 533 TYR 0.016 0.001 TYR B 823 ARG 0.001 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.275 Fit side-chains REVERT: B 358 MET cc_start: 0.5346 (ttm) cc_final: 0.4235 (ttm) REVERT: B 515 ILE cc_start: 0.8958 (mm) cc_final: 0.8730 (mm) REVERT: C 760 ILE cc_start: 0.8978 (mm) cc_final: 0.8496 (pt) REVERT: D 181 ASP cc_start: 0.8104 (p0) cc_final: 0.7223 (t0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2013 time to fit residues: 67.1896 Evaluate side-chains 161 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.0980 chunk 252 optimal weight: 9.9990 chunk 269 optimal weight: 0.8980 chunk 276 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 243 optimal weight: 6.9990 chunk 254 optimal weight: 40.0000 chunk 268 optimal weight: 5.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19011 Z= 0.236 Angle : 0.597 24.622 26305 Z= 0.296 Chirality : 0.060 2.353 3372 Planarity : 0.004 0.071 3431 Dihedral : 4.815 61.368 3208 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -0.59 (0.16), residues: 2948 helix: 1.41 (0.15), residues: 1208 sheet: -2.01 (0.29), residues: 259 loop : -1.68 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 247 HIS 0.003 0.001 HIS A 134 PHE 0.020 0.002 PHE C 533 TYR 0.020 0.002 TYR B 731 ARG 0.001 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.246 Fit side-chains revert: symmetry clash REVERT: B 358 MET cc_start: 0.5422 (ttm) cc_final: 0.4556 (ttm) REVERT: B 515 ILE cc_start: 0.9074 (mm) cc_final: 0.8780 (mm) REVERT: C 760 ILE cc_start: 0.9002 (mm) cc_final: 0.8565 (pt) REVERT: D 181 ASP cc_start: 0.8095 (p0) cc_final: 0.7248 (t0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2256 time to fit residues: 74.4385 Evaluate side-chains 155 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 4.9990 chunk 284 optimal weight: 0.0070 chunk 173 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 198 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19011 Z= 0.172 Angle : 0.568 24.451 26305 Z= 0.276 Chirality : 0.059 2.359 3372 Planarity : 0.004 0.071 3431 Dihedral : 4.522 59.199 3208 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2948 helix: 1.59 (0.16), residues: 1200 sheet: -1.80 (0.30), residues: 257 loop : -1.63 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 247 HIS 0.003 0.001 HIS A 780 PHE 0.016 0.001 PHE C 533 TYR 0.018 0.001 TYR A 681 ARG 0.001 0.000 ARG C 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.152 Fit side-chains REVERT: B 161 MET cc_start: 0.6052 (ttp) cc_final: 0.5693 (ttp) REVERT: B 358 MET cc_start: 0.5402 (ttm) cc_final: 0.4302 (ttm) REVERT: B 515 ILE cc_start: 0.9036 (mm) cc_final: 0.8796 (mm) REVERT: C 760 ILE cc_start: 0.9012 (mm) cc_final: 0.8590 (pt) REVERT: D 181 ASP cc_start: 0.8064 (p0) cc_final: 0.7198 (t0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2049 time to fit residues: 67.8120 Evaluate side-chains 161 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 219 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 238 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 244 optimal weight: 0.5980 chunk 30 optimal weight: 30.0000 chunk 43 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN C 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.084247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.074256 restraints weight = 100434.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.073865 restraints weight = 133493.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.074358 restraints weight = 112996.797| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19011 Z= 0.136 Angle : 0.551 24.424 26305 Z= 0.264 Chirality : 0.059 2.352 3372 Planarity : 0.004 0.069 3431 Dihedral : 4.184 57.859 3208 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.61 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2948 helix: 1.70 (0.15), residues: 1201 sheet: -1.61 (0.30), residues: 267 loop : -1.58 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 607 HIS 0.003 0.001 HIS D 54 PHE 0.015 0.001 PHE C 533 TYR 0.016 0.001 TYR B 823 ARG 0.001 0.000 ARG C 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3216.51 seconds wall clock time: 58 minutes 42.68 seconds (3522.68 seconds total)