Starting phenix.real_space_refine on Mon Jun 16 22:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpu_37724/06_2025/8wpu_37724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpu_37724/06_2025/8wpu_37724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wpu_37724/06_2025/8wpu_37724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpu_37724/06_2025/8wpu_37724.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpu_37724/06_2025/8wpu_37724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpu_37724/06_2025/8wpu_37724.cif" } resolution = 3.1 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= 0.007 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 101 5.16 5 C 12107 2.51 5 N 3124 2.21 5 O 3450 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18794 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6178 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 31, 'TRANS': 776} Chain breaks: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 18, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 172 Chain: "A" Number of atoms: 6169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6169 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 139 Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1619 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2523 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 356 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1643 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 132 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 4, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1106 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 118 Unusual residues: {' CA': 2, 'NAG': 5, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1107 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.59, per 1000 atoms: 0.67 Number of scatterers: 18794 At special positions: 0 Unit cell: (147.66, 120.91, 245.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 101 16.00 P 2 15.00 F 6 9.00 O 3450 8.00 N 3124 7.00 C 12107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1102 " - " ASN A 261 " " NAG A1103 " - " ASN A 287 " " NAG A1104 " - " ASN A 488 " " NAG A1105 " - " ASN A 468 " " NAG A1106 " - " ASN A 594 " " NAG B1101 " - " ASN B 261 " " NAG B1102 " - " ASN B 287 " " NAG B1103 " - " ASN B 468 " " NAG B1104 " - " ASN B 594 " " NAG F 1 " - " ASN B 541 " " NAG H 1 " - " ASN A 541 " Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 2.9 seconds 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 34 sheets defined 39.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.655A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.504A pdb=" N SER B 175 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 4.024A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.865A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.929A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.542A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.828A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 612 through 637 Processing helix chain 'B' and resid 642 through 646 removed outlier: 3.999A pdb=" N ALA B 645 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.673A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 673 through 699 removed outlier: 5.035A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix removed outlier: 3.737A pdb=" N CYS B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.583A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 4.036A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 826 removed outlier: 3.545A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 836 through 861 removed outlier: 3.633A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 868 removed outlier: 4.469A pdb=" N ARG B 866 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 868 " --> pdb=" O SER B 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.813A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.560A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 removed outlier: 4.243A pdb=" N GLN A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.786A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.526A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.564A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.926A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 664 Processing helix chain 'A' and resid 665 through 668 Processing helix chain 'A' and resid 674 through 679 Processing helix chain 'A' and resid 680 through 706 removed outlier: 3.590A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 702 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.672A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 794 removed outlier: 3.903A pdb=" N LEU A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 803 through 821 Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 831 through 862 removed outlier: 3.960A pdb=" N GLU A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 33 removed outlier: 3.767A pdb=" N GLU G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 50 removed outlier: 3.926A pdb=" N GLY G 45 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS G 46 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER G 47 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 130 Processing helix chain 'G' and resid 146 through 154 removed outlier: 4.279A pdb=" N ALA G 150 " --> pdb=" O GLN G 146 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 184 through 202 removed outlier: 3.983A pdb=" N PHE G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG G 194 " --> pdb=" O LYS G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 243 removed outlier: 3.798A pdb=" N ASP G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.695A pdb=" N ASP C 5 " --> pdb=" O GLN C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 removed outlier: 3.768A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.104A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 30 through 44 removed outlier: 3.799A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.518A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.879A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.946A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 319 through 322 removed outlier: 6.574A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.895A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AA7, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AA8, first strand: chain 'B' and resid 590 through 591 Processing sheet with id=AA9, first strand: chain 'B' and resid 602 through 604 removed outlier: 5.534A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.184A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.735A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.772A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.356A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 573 removed outlier: 3.641A pdb=" N TYR A 573 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB9, first strand: chain 'A' and resid 749 through 753 Processing sheet with id=AC1, first strand: chain 'G' and resid 70 through 76 removed outlier: 7.129A pdb=" N ARG G 35 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE G 107 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU G 37 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL G 109 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU G 39 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ASP G 111 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL G 139 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.666A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.694A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.627A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.522A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.667A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.988A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.564A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 315 through 317 Processing sheet with id=AD1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.528A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.528A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 45 through 50 removed outlier: 7.034A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AD5, first strand: chain 'E' and resid 134 through 136 Processing sheet with id=AD6, first strand: chain 'E' and resid 142 through 148 removed outlier: 3.875A pdb=" N VAL E 143 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE E 145 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 174 through 178 removed outlier: 5.062A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2235 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: 7.31 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3169 1.32 - 1.45: 5376 1.45 - 1.57: 10568 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 19238 Sorted by residual: bond pdb=" N ARG B 69 " pdb=" CA ARG B 69 " ideal model delta sigma weight residual 1.459 1.383 0.076 1.17e-02 7.31e+03 4.17e+01 bond pdb=" CA LYS A 805 " pdb=" C LYS A 805 " ideal model delta sigma weight residual 1.524 1.446 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" CA ARG B 69 " pdb=" C ARG B 69 " ideal model delta sigma weight residual 1.524 1.459 0.066 1.24e-02 6.50e+03 2.79e+01 bond pdb=" C ASP C 246 " pdb=" N ASP C 247 " ideal model delta sigma weight residual 1.334 1.275 0.059 1.24e-02 6.50e+03 2.27e+01 bond pdb=" CA ARG A 795 " pdb=" C ARG A 795 " ideal model delta sigma weight residual 1.523 1.462 0.060 1.37e-02 5.33e+03 1.94e+01 ... (remaining 19233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 25722 1.84 - 3.68: 412 3.68 - 5.52: 56 5.52 - 7.36: 15 7.36 - 9.21: 4 Bond angle restraints: 26209 Sorted by residual: angle pdb=" N ARG B 69 " pdb=" CA ARG B 69 " pdb=" C ARG B 69 " ideal model delta sigma weight residual 110.97 102.81 8.16 1.09e+00 8.42e-01 5.61e+01 angle pdb=" CA PRO B 89 " pdb=" N PRO B 89 " pdb=" CD PRO B 89 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" O ILE B 599 " pdb=" C ILE B 599 " pdb=" N ALA B 600 " ideal model delta sigma weight residual 122.97 118.79 4.18 1.07e+00 8.73e-01 1.53e+01 angle pdb=" N ILE A 409 " pdb=" CA ILE A 409 " pdb=" C ILE A 409 " ideal model delta sigma weight residual 113.71 110.13 3.58 9.50e-01 1.11e+00 1.42e+01 angle pdb=" C ARG A 795 " pdb=" CA ARG A 795 " pdb=" CB ARG A 795 " ideal model delta sigma weight residual 110.38 102.80 7.58 2.04e+00 2.40e-01 1.38e+01 ... (remaining 26204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.77: 10920 31.77 - 63.53: 475 63.53 - 95.30: 29 95.30 - 127.06: 7 127.06 - 158.83: 2 Dihedral angle restraints: 11433 sinusoidal: 4313 harmonic: 7120 Sorted by residual: dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 -178.87 -88.13 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual 93.00 159.96 -66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS B 546 " pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " pdb=" CB CYS B 565 " ideal model delta sinusoidal sigma weight residual -86.00 -139.29 53.29 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 11430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2557 0.058 - 0.115: 425 0.115 - 0.173: 39 0.173 - 0.231: 1 0.231 - 0.288: 3 Chirality restraints: 3025 Sorted by residual: chirality pdb=" CB ILE B 741 " pdb=" CA ILE B 741 " pdb=" CG1 ILE B 741 " pdb=" CG2 ILE B 741 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 541 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA YP4 A1110 " pdb=" N YP4 A1110 " pdb=" CB YP4 A1110 " pdb=" C1 YP4 A1110 " both_signs ideal model delta sigma weight residual False -2.41 -2.65 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3022 not shown) Planarity restraints: 3322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 88 " 0.088 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO B 89 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 804 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C ALA A 804 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 804 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 805 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 245 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C SER C 245 " 0.038 2.00e-02 2.50e+03 pdb=" O SER C 245 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 246 " -0.013 2.00e-02 2.50e+03 ... (remaining 3319 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 667 2.71 - 3.26: 19065 3.26 - 3.81: 31260 3.81 - 4.35: 38232 4.35 - 4.90: 65494 Nonbonded interactions: 154718 Sorted by model distance: nonbonded pdb=" O ASP A 570 " pdb=" OG SER A 591 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR G 212 " pdb=" OD1 ASP G 233 " model vdw 2.201 3.040 nonbonded pdb=" O ALA B 548 " pdb=" OG SER B 574 " model vdw 2.204 3.040 nonbonded pdb=" O4 NAG A1106 " pdb=" O7 NAG A1106 " model vdw 2.212 3.040 nonbonded pdb=" O SER A 794 " pdb=" OG SER A 794 " model vdw 2.225 3.040 ... (remaining 154713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 or (resid 61 and (name N or n \ ame CA or name C or name O or name CB )) or resid 62 through 123 or (resid 124 t \ hrough 125 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 230 or (resid 231 and (name N or name CA or name C or n \ ame O or name CB )) or resid 232 through 252 or (resid 253 and (name N or name C \ A or name C or name O or name CB )) or resid 254 through 269 or (resid 270 and ( \ name N or name CA or name C or name O or name CB )) or resid 271 through 296 or \ (resid 297 through 298 and (name N or name CA or name C or name O or name CB )) \ or resid 299 through 393 or (resid 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 432 or (resid 433 and (name N or name CA or \ name C or name O or name CB )) or resid 434 through 450 or (resid 451 and (name \ N or name CA or name C or name O or name CB )) or resid 452 through 454 or (res \ id 455 through 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 461 or (resid 462 and (name N or name CA or name C or name O or \ name CB )) or resid 463 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 518 or (resid 519 and (name N o \ r name CA or name C or name O or name CB )) or resid 520 through 525 or (resid 5 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 527 through \ 543 or (resid 544 and (name N or name CA or name C or name O or name CB )) or r \ esid 545 through 551 or (resid 552 and (name N or name CA or name C or name O or \ name CB )) or resid 553 through 575 or (resid 576 and (name N or name CA or nam \ e C or name O or name CB )) or resid 577 or (resid 578 through 579 and (name N o \ r name CA or name C or name O or name CB )) or resid 580 through 583 or (resid 5 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 585 through \ 586 or (resid 587 through 588 and (name N or name CA or name C or name O or nam \ e CB )) or resid 589 through 591 or (resid 592 through 593 and (name N or name C \ A or name C or name O or name CB )) or resid 594 through 635 or (resid 636 throu \ gh 637 and (name N or name CA or name C or name O or name CB )) or resid 638 thr \ ough 641 or (resid 642 and (name N or name CA or name C or name O or name CB )) \ or resid 643 through 664 or (resid 665 and (name N or name CA or name C or name \ O or name CB )) or resid 666 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 704 or (resid 705 and (name \ N or name CA or name C or name O or name CB )) or resid 719 through 723 or (res \ id 724 and (name N or name CA or name C or name O or name CB )) or resid 725 or \ (resid 726 and (name N or name CA or name C or name O or name CB )) or resid 727 \ through 770 or (resid 771 through 772 and (name N or name CA or name C or name \ O or name CB )) or resid 773 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 through 802 or (resid 803 through 8 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 805 through \ 809 or (resid 810 and (name N or name CA or name C or name O or name CB )) or r \ esid 811 through 862 or (resid 863 and (name N or name CA or name C or name O or \ name CB )) or resid 864 through 865 or resid 1102 through 1105 or resid 1107 th \ rough 1108)) selection = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 131 or (resid 132 thr \ ough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 t \ hrough 322 or (resid 323 through 324 and (name N or name CA or name C or name O \ or name CB )) or resid 325 through 348 or (resid 349 and (name N or name CA or n \ ame C or name O or name CB )) or resid 350 through 360 or (resid 361 and (name N \ or name CA or name C or name O or name CB )) or (resid 392 and (name N or name \ CA or name C or name O or name CB )) or resid 393 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 404 or \ (resid 405 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 6 through 445 or (resid 446 and (name N or name CA or name C or name O or name C \ B )) or resid 447 through 452 or (resid 453 through 457 and (name N or name CA o \ r name C or name O or name CB )) or resid 458 through 475 or (resid 476 and (nam \ e N or name CA or name C or name O or name CB )) or resid 477 through 480 or (re \ sid 481 and (name N or name CA or name C or name O or name CB )) or resid 482 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 535 or (resid 536 and (name N or name CA o \ r name C or name O or name CB )) or resid 537 through 603 or (resid 604 and (nam \ e N or name CA or name C or name O or name CB )) or resid 605 through 609 or (re \ sid 610 and (name N or name CA or name C or name O or name CB )) or resid 611 th \ rough 621 or (resid 622 and (name N or name CA or name C or name O or name CB )) \ or resid 623 through 624 or (resid 625 and (name N or name CA or name C or name \ O or name CB )) or resid 626 through 660 or (resid 661 and (name N or name CA o \ r name C or name O or name CB )) or resid 662 through 670 or (resid 671 and (nam \ e N or name CA or name C or name O or name CB )) or resid 672 through 705 or (re \ sid 719 and (name N or name CA or name C or name O or name CB )) or resid 720 th \ rough 729 or (resid 730 and (name N or name CA or name C or name O or name CB )) \ or resid 731 through 732 or (resid 733 through 734 and (name N or name CA or na \ me C or name O or name CB )) or resid 735 through 736 or (resid 737 and (name N \ or name CA or name C or name O or name CB )) or resid 738 or (resid 739 and (nam \ e N or name CA or name C or name O or name CB )) or resid 740 through 758 or (re \ sid 759 and (name N or name CA or name C or name O or name CB )) or resid 760 th \ rough 792 or (resid 793 through 794 and (name N or name CA or name C or name O o \ r name CB )) or resid 795 through 830 or (resid 831 and (name N or name CA or na \ me C or name O or name CB )) or resid 832 through 865 or resid 1101 through 1104 \ or resid 1106 through 1107)) } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.690 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.004 0.080 19270 Z= 0.210 Angle : 0.591 9.205 26286 Z= 0.318 Chirality : 0.043 0.288 3025 Planarity : 0.004 0.130 3311 Dihedral : 16.874 158.829 6776 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 28.01 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2423 helix: 0.72 (0.18), residues: 830 sheet: -1.22 (0.26), residues: 412 loop : -0.96 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 608 HIS 0.006 0.001 HIS C 142 PHE 0.030 0.001 PHE G 192 TYR 0.021 0.001 TYR E 223 ARG 0.008 0.000 ARG A 752 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 11) link_NAG-ASN : angle 1.78010 ( 33) link_BETA1-4 : bond 0.00064 ( 2) link_BETA1-4 : angle 1.54966 ( 6) hydrogen bonds : bond 0.18807 ( 788) hydrogen bonds : angle 7.10034 ( 2235) SS BOND : bond 0.00130 ( 19) SS BOND : angle 0.44822 ( 38) covalent geometry : bond 0.00399 (19238) covalent geometry : angle 0.58793 (26209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 ASP cc_start: 0.8307 (m-30) cc_final: 0.7913 (t0) REVERT: G 46 LYS cc_start: 0.7992 (mttt) cc_final: 0.7761 (mttt) REVERT: G 244 ASN cc_start: 0.8386 (t0) cc_final: 0.7787 (t0) REVERT: C 264 TYR cc_start: 0.8000 (m-10) cc_final: 0.7698 (m-80) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3212 time to fit residues: 120.9995 Evaluate side-chains 236 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 73 optimal weight: 0.0170 chunk 115 optimal weight: 0.2980 chunk 141 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS A 463 HIS A 466 HIS A 735 GLN A 802 ASN G 123 ASN C 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.096894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082127 restraints weight = 45867.208| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.20 r_work: 0.3306 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19270 Z= 0.129 Angle : 0.544 7.978 26286 Z= 0.286 Chirality : 0.043 0.202 3025 Planarity : 0.004 0.077 3311 Dihedral : 8.623 153.988 2979 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.39 % Allowed : 24.84 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2423 helix: 0.88 (0.18), residues: 844 sheet: -1.19 (0.25), residues: 446 loop : -0.98 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.015 0.001 PHE A 589 TYR 0.021 0.001 TYR E 223 ARG 0.006 0.000 ARG A 752 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 11) link_NAG-ASN : angle 1.45330 ( 33) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 1.18590 ( 6) hydrogen bonds : bond 0.04473 ( 788) hydrogen bonds : angle 5.16159 ( 2235) SS BOND : bond 0.00157 ( 19) SS BOND : angle 0.55849 ( 38) covalent geometry : bond 0.00286 (19238) covalent geometry : angle 0.54144 (26209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 659 LEU cc_start: 0.8701 (mt) cc_final: 0.8412 (mm) REVERT: C 142 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.6421 (t70) REVERT: C 264 TYR cc_start: 0.8302 (m-10) cc_final: 0.7983 (m-80) REVERT: E 6 GLU cc_start: 0.6894 (pm20) cc_final: 0.6646 (pm20) REVERT: E 204 ILE cc_start: 0.4008 (OUTLIER) cc_final: 0.3541 (tt) REVERT: E 223 TYR cc_start: 0.7378 (t80) cc_final: 0.7151 (t80) outliers start: 63 outliers final: 25 residues processed: 288 average time/residue: 0.3126 time to fit residues: 137.1185 Evaluate side-chains 258 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 0.0270 chunk 200 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN B 476 GLN A 260 GLN C 259 GLN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.096741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082077 restraints weight = 45822.023| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.18 r_work: 0.3305 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19270 Z= 0.130 Angle : 0.518 9.381 26286 Z= 0.271 Chirality : 0.042 0.204 3025 Planarity : 0.004 0.057 3311 Dihedral : 7.831 150.279 2979 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.92 % Allowed : 24.25 % Favored : 71.83 % 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: -0.48 (0.17), residues: 2423 helix: 0.98 (0.18), residues: 844 sheet: -1.06 (0.25), residues: 443 loop : -0.94 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.001 PHE A 605 TYR 0.023 0.001 TYR E 223 ARG 0.006 0.000 ARG B 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 11) link_NAG-ASN : angle 1.42893 ( 33) link_BETA1-4 : bond 0.00078 ( 2) link_BETA1-4 : angle 1.24647 ( 6) hydrogen bonds : bond 0.04046 ( 788) hydrogen bonds : angle 4.75907 ( 2235) SS BOND : bond 0.00139 ( 19) SS BOND : angle 0.48504 ( 38) covalent geometry : bond 0.00298 (19238) covalent geometry : angle 0.51575 (26209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 243 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 589 PHE cc_start: 0.8612 (m-80) cc_final: 0.8360 (m-80) REVERT: B 686 ILE cc_start: 0.7159 (pt) cc_final: 0.6734 (mm) REVERT: G 53 MET cc_start: 0.5692 (mtm) cc_final: 0.4826 (ttt) REVERT: G 148 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5649 (pt) REVERT: C 142 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6867 (t70) REVERT: C 262 MET cc_start: 0.7232 (tpp) cc_final: 0.6758 (tpp) REVERT: C 264 TYR cc_start: 0.8296 (m-10) cc_final: 0.8009 (m-80) REVERT: E 204 ILE cc_start: 0.4000 (OUTLIER) cc_final: 0.3494 (tt) REVERT: E 223 TYR cc_start: 0.7393 (t80) cc_final: 0.7076 (t80) outliers start: 73 outliers final: 36 residues processed: 294 average time/residue: 0.3162 time to fit residues: 142.1319 Evaluate side-chains 271 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 182 optimal weight: 0.1980 chunk 232 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 238 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 150 optimal weight: 0.0670 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082992 restraints weight = 46052.164| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.21 r_work: 0.3325 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19270 Z= 0.103 Angle : 0.499 10.839 26286 Z= 0.261 Chirality : 0.041 0.217 3025 Planarity : 0.004 0.048 3311 Dihedral : 7.235 147.055 2979 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.98 % Allowed : 23.76 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2423 helix: 1.12 (0.18), residues: 840 sheet: -1.06 (0.25), residues: 437 loop : -0.94 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.020 0.001 PHE A 789 TYR 0.024 0.001 TYR E 223 ARG 0.007 0.000 ARG A 752 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 11) link_NAG-ASN : angle 1.52288 ( 33) link_BETA1-4 : bond 0.00237 ( 2) link_BETA1-4 : angle 1.18127 ( 6) hydrogen bonds : bond 0.03604 ( 788) hydrogen bonds : angle 4.50646 ( 2235) SS BOND : bond 0.00143 ( 19) SS BOND : angle 0.55307 ( 38) covalent geometry : bond 0.00231 (19238) covalent geometry : angle 0.49641 (26209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 243 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 PHE cc_start: 0.8605 (m-80) cc_final: 0.8355 (m-80) REVERT: B 686 ILE cc_start: 0.7194 (pt) cc_final: 0.6782 (mm) REVERT: A 425 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7689 (m-10) REVERT: A 751 TYR cc_start: 0.7882 (t80) cc_final: 0.7596 (t80) REVERT: G 23 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8390 (mt) REVERT: G 46 LYS cc_start: 0.7893 (mttt) cc_final: 0.7663 (mttt) REVERT: G 53 MET cc_start: 0.5413 (mtm) cc_final: 0.4677 (ttt) REVERT: G 151 GLU cc_start: 0.3321 (tp30) cc_final: 0.2916 (tp30) REVERT: G 244 ASN cc_start: 0.8619 (t0) cc_final: 0.8055 (t0) REVERT: C 142 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.6688 (t70) REVERT: C 264 TYR cc_start: 0.8327 (m-10) cc_final: 0.8056 (m-80) REVERT: E 7 SER cc_start: 0.7945 (m) cc_final: 0.7564 (p) REVERT: E 204 ILE cc_start: 0.3883 (OUTLIER) cc_final: 0.3390 (tt) REVERT: E 223 TYR cc_start: 0.7355 (t80) cc_final: 0.7023 (t80) outliers start: 74 outliers final: 44 residues processed: 292 average time/residue: 0.3601 time to fit residues: 165.3809 Evaluate side-chains 276 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 203 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 0.0030 chunk 139 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.096211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081405 restraints weight = 46251.771| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.21 r_work: 0.3293 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19270 Z= 0.153 Angle : 0.526 9.801 26286 Z= 0.274 Chirality : 0.042 0.218 3025 Planarity : 0.004 0.047 3311 Dihedral : 6.802 146.087 2979 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.14 % Allowed : 23.55 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2423 helix: 1.07 (0.18), residues: 846 sheet: -1.02 (0.25), residues: 457 loop : -0.93 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.028 0.001 PHE A 605 TYR 0.026 0.001 TYR E 223 ARG 0.007 0.000 ARG C 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 11) link_NAG-ASN : angle 2.27348 ( 33) link_BETA1-4 : bond 0.00093 ( 2) link_BETA1-4 : angle 1.30478 ( 6) hydrogen bonds : bond 0.03823 ( 788) hydrogen bonds : angle 4.52750 ( 2235) SS BOND : bond 0.00159 ( 19) SS BOND : angle 0.51473 ( 38) covalent geometry : bond 0.00357 (19238) covalent geometry : angle 0.52002 (26209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 237 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.8640 (ttt) cc_final: 0.8422 (ttm) REVERT: B 589 PHE cc_start: 0.8635 (m-80) cc_final: 0.8372 (m-80) REVERT: B 603 ILE cc_start: 0.8804 (mm) cc_final: 0.8498 (mt) REVERT: B 686 ILE cc_start: 0.7379 (pt) cc_final: 0.6976 (mm) REVERT: A 425 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7852 (m-10) REVERT: A 751 TYR cc_start: 0.7996 (t80) cc_final: 0.7795 (t80) REVERT: G 8 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: G 23 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8383 (mt) REVERT: G 53 MET cc_start: 0.5412 (mtm) cc_final: 0.4662 (ttt) REVERT: G 142 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: G 151 GLU cc_start: 0.3605 (tp30) cc_final: 0.3196 (tp30) REVERT: G 244 ASN cc_start: 0.8622 (t0) cc_final: 0.8051 (t0) REVERT: C 262 MET cc_start: 0.7124 (tpp) cc_final: 0.6881 (tpp) REVERT: C 264 TYR cc_start: 0.8327 (m-10) cc_final: 0.8073 (m-80) REVERT: E 7 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7610 (p) REVERT: E 204 ILE cc_start: 0.4054 (OUTLIER) cc_final: 0.3555 (tt) REVERT: E 223 TYR cc_start: 0.7416 (t80) cc_final: 0.7175 (t80) outliers start: 77 outliers final: 49 residues processed: 290 average time/residue: 0.3190 time to fit residues: 146.2612 Evaluate side-chains 287 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 0 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.096316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081574 restraints weight = 46242.323| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.21 r_work: 0.3296 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19270 Z= 0.139 Angle : 0.514 7.504 26286 Z= 0.270 Chirality : 0.042 0.223 3025 Planarity : 0.004 0.046 3311 Dihedral : 6.554 142.176 2979 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.09 % Allowed : 24.19 % Favored : 71.72 % 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 (0.17), residues: 2423 helix: 1.07 (0.18), residues: 847 sheet: -1.00 (0.25), residues: 456 loop : -0.94 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.026 0.001 PHE A 605 TYR 0.027 0.001 TYR E 223 ARG 0.006 0.000 ARG C 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 11) link_NAG-ASN : angle 1.98828 ( 33) link_BETA1-4 : bond 0.00127 ( 2) link_BETA1-4 : angle 1.21135 ( 6) hydrogen bonds : bond 0.03738 ( 788) hydrogen bonds : angle 4.45467 ( 2235) SS BOND : bond 0.00157 ( 19) SS BOND : angle 0.49778 ( 38) covalent geometry : bond 0.00322 (19238) covalent geometry : angle 0.50932 (26209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.8646 (ttt) cc_final: 0.8426 (ttm) REVERT: B 95 TYR cc_start: 0.8192 (p90) cc_final: 0.7957 (p90) REVERT: B 589 PHE cc_start: 0.8624 (m-80) cc_final: 0.8362 (m-80) REVERT: B 603 ILE cc_start: 0.8831 (mm) cc_final: 0.8551 (mt) REVERT: B 684 PHE cc_start: 0.7396 (t80) cc_final: 0.7187 (t80) REVERT: B 686 ILE cc_start: 0.7196 (pt) cc_final: 0.6795 (mm) REVERT: A 425 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7848 (m-10) REVERT: A 751 TYR cc_start: 0.7994 (t80) cc_final: 0.7764 (t80) REVERT: G 8 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: G 23 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8385 (mt) REVERT: G 53 MET cc_start: 0.5394 (mtm) cc_final: 0.4686 (ttt) REVERT: G 142 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7686 (m-10) REVERT: G 151 GLU cc_start: 0.3517 (tp30) cc_final: 0.3143 (tp30) REVERT: G 244 ASN cc_start: 0.8622 (t0) cc_final: 0.8043 (t0) REVERT: C 262 MET cc_start: 0.7115 (tpp) cc_final: 0.6873 (tpp) REVERT: C 264 TYR cc_start: 0.8318 (m-10) cc_final: 0.8073 (m-80) REVERT: E 7 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7622 (p) REVERT: E 34 MET cc_start: 0.8261 (mmm) cc_final: 0.8047 (mmm) REVERT: E 204 ILE cc_start: 0.4007 (OUTLIER) cc_final: 0.3512 (tt) REVERT: E 223 TYR cc_start: 0.7380 (t80) cc_final: 0.7173 (t80) outliers start: 76 outliers final: 54 residues processed: 296 average time/residue: 0.3031 time to fit residues: 138.5305 Evaluate side-chains 292 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 232 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 640 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.094318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079491 restraints weight = 45630.141| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.19 r_work: 0.3253 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19270 Z= 0.229 Angle : 0.580 6.955 26286 Z= 0.305 Chirality : 0.045 0.227 3025 Planarity : 0.004 0.047 3311 Dihedral : 6.634 132.726 2979 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.84 % Allowed : 23.60 % Favored : 71.56 % 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: -0.58 (0.17), residues: 2423 helix: 0.85 (0.18), residues: 858 sheet: -1.07 (0.25), residues: 441 loop : -1.01 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 530 HIS 0.007 0.001 HIS E 35 PHE 0.029 0.002 PHE G 192 TYR 0.030 0.002 TYR E 223 ARG 0.007 0.001 ARG B 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 11) link_NAG-ASN : angle 2.02977 ( 33) link_BETA1-4 : bond 0.00165 ( 2) link_BETA1-4 : angle 1.34284 ( 6) hydrogen bonds : bond 0.04285 ( 788) hydrogen bonds : angle 4.66192 ( 2235) SS BOND : bond 0.00233 ( 19) SS BOND : angle 0.64422 ( 38) covalent geometry : bond 0.00531 (19238) covalent geometry : angle 0.57550 (26209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 233 time to evaluate : 2.228 Fit side-chains revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8209 (p90) cc_final: 0.7966 (p90) REVERT: B 603 ILE cc_start: 0.8826 (mm) cc_final: 0.8604 (tp) REVERT: B 686 ILE cc_start: 0.7399 (pt) cc_final: 0.6962 (mm) REVERT: A 425 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7975 (m-10) REVERT: A 680 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7841 (mtp180) REVERT: G 8 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: G 23 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8392 (mt) REVERT: G 53 MET cc_start: 0.5470 (mtm) cc_final: 0.4761 (ttt) REVERT: G 142 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7779 (m-10) REVERT: G 244 ASN cc_start: 0.8649 (t0) cc_final: 0.8030 (t0) REVERT: C 44 GLN cc_start: 0.7369 (pp30) cc_final: 0.7163 (pp30) REVERT: C 234 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8516 (t80) REVERT: C 264 TYR cc_start: 0.8322 (m-10) cc_final: 0.8097 (m-80) REVERT: C 289 TYR cc_start: 0.8232 (m-80) cc_final: 0.8021 (m-80) REVERT: D 29 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7428 (ttmm) outliers start: 90 outliers final: 61 residues processed: 304 average time/residue: 0.2928 time to fit residues: 138.4241 Evaluate side-chains 299 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 193 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 236 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080387 restraints weight = 46064.283| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.22 r_work: 0.3273 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19270 Z= 0.158 Angle : 0.542 8.830 26286 Z= 0.283 Chirality : 0.043 0.243 3025 Planarity : 0.004 0.046 3311 Dihedral : 6.447 122.721 2979 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.98 % Allowed : 24.46 % Favored : 71.56 % 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: -0.55 (0.17), residues: 2423 helix: 0.96 (0.18), residues: 848 sheet: -1.10 (0.25), residues: 446 loop : -1.02 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.029 0.001 PHE G 192 TYR 0.025 0.001 TYR E 223 ARG 0.007 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 11) link_NAG-ASN : angle 1.79105 ( 33) link_BETA1-4 : bond 0.00179 ( 2) link_BETA1-4 : angle 1.30377 ( 6) hydrogen bonds : bond 0.03904 ( 788) hydrogen bonds : angle 4.52250 ( 2235) SS BOND : bond 0.00177 ( 19) SS BOND : angle 0.52528 ( 38) covalent geometry : bond 0.00368 (19238) covalent geometry : angle 0.53802 (26209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 239 time to evaluate : 2.171 Fit side-chains revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8219 (p90) cc_final: 0.8018 (p90) REVERT: B 589 PHE cc_start: 0.8643 (m-80) cc_final: 0.8378 (m-80) REVERT: B 686 ILE cc_start: 0.7411 (pt) cc_final: 0.6981 (mm) REVERT: A 425 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7996 (m-10) REVERT: G 8 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: G 23 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8404 (mt) REVERT: G 53 MET cc_start: 0.5456 (mtm) cc_final: 0.4786 (ttt) REVERT: G 142 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7693 (m-10) REVERT: G 244 ASN cc_start: 0.8627 (t0) cc_final: 0.8030 (t0) REVERT: C 44 GLN cc_start: 0.7332 (pp30) cc_final: 0.7124 (pp30) REVERT: C 234 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8543 (t80) REVERT: C 264 TYR cc_start: 0.8291 (m-10) cc_final: 0.8071 (m-80) REVERT: C 289 TYR cc_start: 0.8227 (m-80) cc_final: 0.8008 (m-80) REVERT: D 29 LYS cc_start: 0.7602 (ttmm) cc_final: 0.7351 (ttmm) REVERT: E 7 SER cc_start: 0.8075 (m) cc_final: 0.7632 (p) REVERT: E 204 ILE cc_start: 0.4115 (OUTLIER) cc_final: 0.3594 (tt) REVERT: E 214 VAL cc_start: 0.7846 (m) cc_final: 0.7514 (p) outliers start: 74 outliers final: 59 residues processed: 296 average time/residue: 0.3011 time to fit residues: 140.0348 Evaluate side-chains 296 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 232 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.095859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080963 restraints weight = 46277.672| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.22 r_work: 0.3285 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19270 Z= 0.138 Angle : 0.535 8.383 26286 Z= 0.280 Chirality : 0.043 0.247 3025 Planarity : 0.004 0.045 3311 Dihedral : 6.252 115.178 2979 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.19 % Allowed : 24.41 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2423 helix: 0.96 (0.18), residues: 854 sheet: -1.11 (0.25), residues: 448 loop : -0.98 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.031 0.001 PHE G 192 TYR 0.021 0.001 TYR E 223 ARG 0.007 0.000 ARG C 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 11) link_NAG-ASN : angle 1.65938 ( 33) link_BETA1-4 : bond 0.00107 ( 2) link_BETA1-4 : angle 1.26166 ( 6) hydrogen bonds : bond 0.03749 ( 788) hydrogen bonds : angle 4.43121 ( 2235) SS BOND : bond 0.00241 ( 19) SS BOND : angle 0.73435 ( 38) covalent geometry : bond 0.00321 (19238) covalent geometry : angle 0.53154 (26209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 237 time to evaluate : 2.124 Fit side-chains revert: symmetry clash REVERT: B 74 MET cc_start: 0.8630 (ttt) cc_final: 0.8398 (ttm) REVERT: B 589 PHE cc_start: 0.8631 (m-80) cc_final: 0.8378 (m-80) REVERT: B 686 ILE cc_start: 0.7391 (pt) cc_final: 0.6983 (mm) REVERT: A 425 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.8011 (m-10) REVERT: G 8 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: G 23 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8395 (mt) REVERT: G 53 MET cc_start: 0.5357 (mtm) cc_final: 0.4663 (ttt) REVERT: G 142 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7693 (m-10) REVERT: G 244 ASN cc_start: 0.8591 (t0) cc_final: 0.7989 (t0) REVERT: C 44 GLN cc_start: 0.7351 (pp30) cc_final: 0.7131 (pp30) REVERT: C 264 TYR cc_start: 0.8303 (m-10) cc_final: 0.8032 (m-80) REVERT: C 289 TYR cc_start: 0.8226 (m-80) cc_final: 0.7982 (m-80) REVERT: D 29 LYS cc_start: 0.7528 (ttmm) cc_final: 0.7287 (ttmm) REVERT: E 7 SER cc_start: 0.8046 (m) cc_final: 0.7606 (p) REVERT: E 204 ILE cc_start: 0.4055 (OUTLIER) cc_final: 0.3522 (tt) REVERT: E 214 VAL cc_start: 0.7852 (m) cc_final: 0.7513 (p) REVERT: E 223 TYR cc_start: 0.7395 (t80) cc_final: 0.7068 (t80) outliers start: 78 outliers final: 63 residues processed: 295 average time/residue: 0.2848 time to fit residues: 131.6538 Evaluate side-chains 300 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 190 optimal weight: 0.0170 chunk 173 optimal weight: 0.9990 chunk 167 optimal weight: 0.0470 chunk 176 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.096541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.081881 restraints weight = 45943.278| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.20 r_work: 0.3303 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19270 Z= 0.120 Angle : 0.521 8.542 26286 Z= 0.271 Chirality : 0.042 0.254 3025 Planarity : 0.004 0.045 3311 Dihedral : 5.981 109.043 2979 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.55 % Allowed : 25.11 % Favored : 71.34 % 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 (0.17), residues: 2423 helix: 1.01 (0.18), residues: 855 sheet: -1.10 (0.25), residues: 449 loop : -0.93 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.029 0.001 PHE G 192 TYR 0.020 0.001 TYR E 223 ARG 0.007 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 11) link_NAG-ASN : angle 1.53751 ( 33) link_BETA1-4 : bond 0.00203 ( 2) link_BETA1-4 : angle 1.22428 ( 6) hydrogen bonds : bond 0.03576 ( 788) hydrogen bonds : angle 4.34212 ( 2235) SS BOND : bond 0.00147 ( 19) SS BOND : angle 0.65246 ( 38) covalent geometry : bond 0.00277 (19238) covalent geometry : angle 0.51789 (26209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: B 74 MET cc_start: 0.8628 (ttt) cc_final: 0.8419 (ttm) REVERT: B 589 PHE cc_start: 0.8633 (m-80) cc_final: 0.8377 (m-80) REVERT: B 686 ILE cc_start: 0.7390 (pt) cc_final: 0.6986 (mm) REVERT: A 425 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7890 (m-10) REVERT: G 8 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: G 53 MET cc_start: 0.5322 (mtm) cc_final: 0.4649 (ttt) REVERT: G 244 ASN cc_start: 0.8602 (t0) cc_final: 0.8004 (t0) REVERT: C 44 GLN cc_start: 0.7274 (pp30) cc_final: 0.7038 (pp30) REVERT: C 264 TYR cc_start: 0.8173 (m-10) cc_final: 0.7835 (m-80) REVERT: D 29 LYS cc_start: 0.7414 (ttmm) cc_final: 0.7167 (ttmm) REVERT: E 7 SER cc_start: 0.8013 (m) cc_final: 0.7607 (p) REVERT: E 46 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7176 (mm-30) REVERT: E 204 ILE cc_start: 0.4043 (OUTLIER) cc_final: 0.3512 (tt) REVERT: E 214 VAL cc_start: 0.7857 (m) cc_final: 0.7518 (p) REVERT: E 223 TYR cc_start: 0.7278 (t80) cc_final: 0.6833 (t80) outliers start: 66 outliers final: 56 residues processed: 283 average time/residue: 0.2891 time to fit residues: 127.2488 Evaluate side-chains 289 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 168 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 208 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 184 optimal weight: 0.0020 chunk 15 optimal weight: 0.5980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.096232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081544 restraints weight = 45783.720| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.20 r_work: 0.3297 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19270 Z= 0.134 Angle : 0.528 9.257 26286 Z= 0.275 Chirality : 0.042 0.245 3025 Planarity : 0.004 0.045 3311 Dihedral : 5.926 113.545 2979 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.55 % Allowed : 25.22 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2423 helix: 1.05 (0.18), residues: 851 sheet: -1.12 (0.25), residues: 452 loop : -0.93 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.030 0.001 PHE G 192 TYR 0.020 0.001 TYR E 223 ARG 0.008 0.000 ARG B 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 11) link_NAG-ASN : angle 1.52867 ( 33) link_BETA1-4 : bond 0.00148 ( 2) link_BETA1-4 : angle 1.23030 ( 6) hydrogen bonds : bond 0.03635 ( 788) hydrogen bonds : angle 4.34427 ( 2235) SS BOND : bond 0.00158 ( 19) SS BOND : angle 0.60750 ( 38) covalent geometry : bond 0.00313 (19238) covalent geometry : angle 0.52548 (26209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14100.96 seconds wall clock time: 246 minutes 24.92 seconds (14784.92 seconds total)