Starting phenix.real_space_refine on Mon May 19 23:21:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpu_37724/05_2025/8wpu_37724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpu_37724/05_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_37724/05_2025/8wpu_37724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpu_37724/05_2025/8wpu_37724.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpu_37724/05_2025/8wpu_37724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpu_37724/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.96, per 1000 atoms: 0.58 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: 4.81 Conformation dependent library (CDL) restraints added in 2.5 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: 2.34 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: 6.61 Time building geometry restraints manager: 5.57 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: 4.880 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.350 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.690 ------------------------------------------------------------------------------- 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 : 1.996 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: 0.3056 time to fit residues: 114.5861 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 : 2.095 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.096881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082092 restraints weight = 45850.057| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.21 r_work: 0.3306 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0761 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 7.971 26286 Z= 0.286 Chirality : 0.043 0.202 3025 Planarity : 0.004 0.077 3311 Dihedral : 8.624 153.993 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: -1.21 (0.25), residues: 448 loop : -0.98 (0.19), residues: 1131 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 0.00419 ( 11) link_NAG-ASN : angle 1.45368 ( 33) link_BETA1-4 : bond 0.00411 ( 2) link_BETA1-4 : angle 1.18347 ( 6) hydrogen bonds : bond 0.04473 ( 788) hydrogen bonds : angle 5.16187 ( 2235) SS BOND : bond 0.00157 ( 19) SS BOND : angle 0.55824 ( 38) covalent geometry : bond 0.00286 (19238) covalent geometry : angle 0.54147 (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 : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 659 LEU cc_start: 0.8702 (mt) cc_final: 0.8413 (mm) REVERT: C 142 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.6421 (t70) REVERT: C 264 TYR cc_start: 0.8300 (m-10) cc_final: 0.7980 (m-80) REVERT: E 6 GLU cc_start: 0.6897 (pm20) cc_final: 0.6647 (pm20) REVERT: E 204 ILE cc_start: 0.4015 (OUTLIER) cc_final: 0.3543 (tt) REVERT: E 223 TYR cc_start: 0.7376 (t80) cc_final: 0.7150 (t80) outliers start: 63 outliers final: 25 residues processed: 288 average time/residue: 0.2969 time to fit residues: 129.8311 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 : 1.976 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.1980 chunk 2 optimal weight: 0.1980 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: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN A 260 GLN C 259 GLN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.096892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082241 restraints weight = 45835.170| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.17 r_work: 0.3308 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1028 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= 0.125 Angle : 0.517 9.222 26286 Z= 0.271 Chirality : 0.042 0.207 3025 Planarity : 0.004 0.055 3311 Dihedral : 7.900 150.796 2979 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.98 % Allowed : 24.14 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2423 helix: 0.98 (0.18), residues: 844 sheet: -1.10 (0.25), residues: 441 loop : -0.95 (0.19), residues: 1138 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 0.015 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 0.00310 ( 11) link_NAG-ASN : angle 1.39457 ( 33) link_BETA1-4 : bond 0.00154 ( 2) link_BETA1-4 : angle 1.24041 ( 6) hydrogen bonds : bond 0.04019 ( 788) hydrogen bonds : angle 4.77951 ( 2235) SS BOND : bond 0.00134 ( 19) SS BOND : angle 0.47743 ( 38) covalent geometry : bond 0.00286 (19238) covalent geometry : angle 0.51480 (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 317 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 243 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 589 PHE cc_start: 0.8595 (m-80) cc_final: 0.8347 (m-80) REVERT: B 686 ILE cc_start: 0.7256 (pt) cc_final: 0.6827 (mm) REVERT: G 53 MET cc_start: 0.5698 (mtm) cc_final: 0.4849 (ttt) REVERT: G 148 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5624 (pt) REVERT: C 142 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.6817 (t70) REVERT: C 262 MET cc_start: 0.7206 (tpp) cc_final: 0.6749 (tpp) REVERT: C 264 TYR cc_start: 0.8310 (m-10) cc_final: 0.8018 (m-80) REVERT: E 204 ILE cc_start: 0.4013 (OUTLIER) cc_final: 0.3505 (tt) REVERT: E 223 TYR cc_start: 0.7418 (t80) cc_final: 0.7102 (t80) outliers start: 74 outliers final: 39 residues processed: 293 average time/residue: 0.3021 time to fit residues: 135.1934 Evaluate side-chains 271 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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 609 THR 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 809 PHE 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 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 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: 2.9990 chunk 232 optimal weight: 4.9990 chunk 227 optimal weight: 0.7980 chunk 238 optimal weight: 0.0050 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 GLN ** 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 = 0.3677 r_free = 0.3677 target = 0.096591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081816 restraints weight = 46002.014| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.21 r_work: 0.3301 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19270 Z= 0.133 Angle : 0.512 10.602 26286 Z= 0.269 Chirality : 0.042 0.212 3025 Planarity : 0.004 0.047 3311 Dihedral : 7.392 149.262 2979 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.19 % Allowed : 23.82 % 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: -0.45 (0.17), residues: 2423 helix: 1.05 (0.18), residues: 841 sheet: -1.03 (0.25), residues: 446 loop : -0.97 (0.19), residues: 1136 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 0.020 0.001 PHE A 789 TYR 0.026 0.001 TYR E 223 ARG 0.006 0.000 ARG A 752 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 11) link_NAG-ASN : angle 1.55771 ( 33) link_BETA1-4 : bond 0.00137 ( 2) link_BETA1-4 : angle 1.23749 ( 6) hydrogen bonds : bond 0.03830 ( 788) hydrogen bonds : angle 4.60330 ( 2235) SS BOND : bond 0.00269 ( 19) SS BOND : angle 0.49825 ( 38) covalent geometry : bond 0.00306 (19238) covalent geometry : angle 0.50921 (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 316 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 238 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 589 PHE cc_start: 0.8627 (m-80) cc_final: 0.8368 (m-80) REVERT: B 684 PHE cc_start: 0.7405 (t80) cc_final: 0.7190 (t80) REVERT: B 686 ILE cc_start: 0.7175 (pt) cc_final: 0.6762 (mm) REVERT: A 425 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7718 (m-10) REVERT: A 751 TYR cc_start: 0.7879 (t80) cc_final: 0.7591 (t80) REVERT: G 23 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8388 (mt) REVERT: G 53 MET cc_start: 0.5464 (mtm) cc_final: 0.4745 (ttt) REVERT: G 142 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: G 148 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5682 (pt) REVERT: G 151 GLU cc_start: 0.3601 (tp30) cc_final: 0.3143 (tp30) REVERT: C 142 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.6891 (t70) REVERT: C 264 TYR cc_start: 0.8320 (m-10) cc_final: 0.8049 (m-80) REVERT: E 204 ILE cc_start: 0.3969 (OUTLIER) cc_final: 0.3468 (tt) REVERT: E 223 TYR cc_start: 0.7390 (t80) cc_final: 0.7141 (t80) outliers start: 78 outliers final: 48 residues processed: 290 average time/residue: 0.2967 time to fit residues: 133.1809 Evaluate side-chains 282 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 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 223 ILE Chi-restraints excluded: chain B residue 409 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 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 697 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE 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 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 669 ILE 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 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 148 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- 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: 0.2980 chunk 145 optimal weight: 0.2980 chunk 139 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 241 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 476 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 = 0.3683 r_free = 0.3683 target = 0.096949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082197 restraints weight = 46228.015| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.22 r_work: 0.3309 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1340 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= 0.119 Angle : 0.510 10.390 26286 Z= 0.265 Chirality : 0.042 0.225 3025 Planarity : 0.004 0.047 3311 Dihedral : 6.716 137.838 2979 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.30 % Allowed : 23.60 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2423 helix: 1.06 (0.18), residues: 849 sheet: -0.98 (0.25), residues: 457 loop : -0.93 (0.19), residues: 1117 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 0.028 0.001 PHE A 605 TYR 0.025 0.001 TYR E 223 ARG 0.007 0.000 ARG C 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 11) link_NAG-ASN : angle 2.18043 ( 33) link_BETA1-4 : bond 0.00122 ( 2) link_BETA1-4 : angle 1.27861 ( 6) hydrogen bonds : bond 0.03656 ( 788) hydrogen bonds : angle 4.47371 ( 2235) SS BOND : bond 0.00135 ( 19) SS BOND : angle 0.46020 ( 38) covalent geometry : bond 0.00272 (19238) covalent geometry : angle 0.50371 (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 317 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 237 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 589 PHE cc_start: 0.8612 (m-80) cc_final: 0.8349 (m-80) REVERT: B 603 ILE cc_start: 0.8795 (mm) cc_final: 0.8491 (mt) REVERT: B 686 ILE cc_start: 0.7198 (pt) cc_final: 0.6804 (mm) REVERT: A 425 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7767 (m-10) REVERT: A 562 CYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7255 (m) REVERT: G 8 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: G 23 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8387 (mt) REVERT: G 46 LYS cc_start: 0.7873 (mttt) cc_final: 0.7654 (mttt) REVERT: G 53 MET cc_start: 0.5408 (mtm) cc_final: 0.4627 (ttt) REVERT: G 148 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5704 (pt) REVERT: G 151 GLU cc_start: 0.3431 (tp30) cc_final: 0.3030 (tp30) REVERT: G 244 ASN cc_start: 0.8627 (t0) cc_final: 0.8063 (t0) REVERT: C 264 TYR cc_start: 0.8309 (m-10) cc_final: 0.8050 (m-80) REVERT: E 7 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7592 (p) REVERT: E 204 ILE cc_start: 0.3924 (OUTLIER) cc_final: 0.3426 (tt) REVERT: E 223 TYR cc_start: 0.7385 (t80) cc_final: 0.7106 (t80) outliers start: 80 outliers final: 52 residues processed: 292 average time/residue: 0.3065 time to fit residues: 139.5391 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 : 2.030 ------------------------------------------------------------------------------- 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 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 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 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 665 SER 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 809 PHE Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 859 ILE 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 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 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 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 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: 0.0980 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 167 optimal weight: 0.1980 chunk 223 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.096867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082152 restraints weight = 46222.051| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.22 r_work: 0.3307 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1438 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= 0.123 Angle : 0.503 6.934 26286 Z= 0.263 Chirality : 0.042 0.226 3025 Planarity : 0.004 0.047 3311 Dihedral : 6.477 137.788 2979 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.98 % Allowed : 24.19 % 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: -0.37 (0.17), residues: 2423 helix: 1.11 (0.18), residues: 844 sheet: -0.98 (0.25), residues: 457 loop : -0.92 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.026 0.001 PHE A 605 TYR 0.026 0.001 TYR E 223 ARG 0.006 0.000 ARG B 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 11) link_NAG-ASN : angle 2.03146 ( 33) link_BETA1-4 : bond 0.00166 ( 2) link_BETA1-4 : angle 1.19135 ( 6) hydrogen bonds : bond 0.03630 ( 788) hydrogen bonds : angle 4.41331 ( 2235) SS BOND : bond 0.00142 ( 19) SS BOND : angle 0.45855 ( 38) covalent geometry : bond 0.00283 (19238) covalent geometry : angle 0.49781 (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 311 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 237 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8197 (p90) cc_final: 0.7975 (p90) REVERT: B 589 PHE cc_start: 0.8620 (m-80) cc_final: 0.8353 (m-80) REVERT: B 603 ILE cc_start: 0.8841 (mm) cc_final: 0.8551 (mt) REVERT: B 686 ILE cc_start: 0.7206 (pt) cc_final: 0.6792 (mm) REVERT: A 425 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7891 (m-10) REVERT: A 562 CYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7280 (m) REVERT: G 8 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: G 23 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8389 (mt) REVERT: G 46 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7684 (mttt) REVERT: G 53 MET cc_start: 0.5396 (mtm) cc_final: 0.4686 (ttt) REVERT: G 148 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5770 (pt) REVERT: G 151 GLU cc_start: 0.3444 (tp30) cc_final: 0.3085 (tp30) REVERT: G 244 ASN cc_start: 0.8621 (t0) cc_final: 0.8058 (t0) REVERT: C 264 TYR cc_start: 0.8306 (m-10) cc_final: 0.8026 (m-80) REVERT: E 7 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7599 (p) REVERT: E 34 MET cc_start: 0.8257 (mmm) cc_final: 0.8043 (mmm) REVERT: E 204 ILE cc_start: 0.3981 (OUTLIER) cc_final: 0.3492 (tt) REVERT: E 223 TYR cc_start: 0.7375 (t80) cc_final: 0.7139 (t80) outliers start: 74 outliers final: 50 residues processed: 288 average time/residue: 0.2911 time to fit residues: 131.1517 Evaluate side-chains 290 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 2.116 ------------------------------------------------------------------------------- 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 434 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 481 GLU 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 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 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 23 LEU Chi-restraints excluded: chain G residue 46 LYS 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 47 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 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: 3.9990 chunk 187 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 1 optimal weight: 0.0040 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN A 179 GLN A 260 GLN C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.093584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.078750 restraints weight = 45732.963| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.18 r_work: 0.3235 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 19270 Z= 0.284 Angle : 0.628 6.883 26286 Z= 0.331 Chirality : 0.046 0.239 3025 Planarity : 0.004 0.048 3311 Dihedral : 6.878 140.046 2979 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.68 % Allowed : 23.66 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 2423 helix: 0.74 (0.18), residues: 861 sheet: -1.14 (0.25), residues: 455 loop : -1.07 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 818 HIS 0.008 0.001 HIS E 35 PHE 0.028 0.002 PHE G 192 TYR 0.034 0.002 TYR E 223 ARG 0.008 0.001 ARG A 752 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 11) link_NAG-ASN : angle 2.20311 ( 33) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.41648 ( 6) hydrogen bonds : bond 0.04593 ( 788) hydrogen bonds : angle 4.78664 ( 2235) SS BOND : bond 0.00286 ( 19) SS BOND : angle 0.75279 ( 38) covalent geometry : bond 0.00658 (19238) covalent geometry : angle 0.62322 (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 320 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 233 time to evaluate : 2.041 Fit side-chains revert: symmetry clash REVERT: B 603 ILE cc_start: 0.8836 (mm) cc_final: 0.8608 (tp) REVERT: B 686 ILE cc_start: 0.7385 (pt) cc_final: 0.6955 (mm) REVERT: A 425 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7946 (m-10) REVERT: A 680 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7878 (mtp180) REVERT: G 8 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: G 142 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7804 (m-10) REVERT: G 244 ASN cc_start: 0.8642 (t0) cc_final: 0.7998 (t0) REVERT: C 44 GLN cc_start: 0.7364 (pp30) cc_final: 0.7154 (pp30) REVERT: C 289 TYR cc_start: 0.8239 (m-80) cc_final: 0.8030 (m-80) outliers start: 87 outliers final: 59 residues processed: 302 average time/residue: 0.2929 time to fit residues: 137.5828 Evaluate side-chains 288 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 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 317 THR 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 193 optimal weight: 0.5980 chunk 162 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 236 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 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 = 0.3658 r_free = 0.3658 target = 0.095558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.080832 restraints weight = 46020.386| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.21 r_work: 0.3278 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1593 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= 0.140 Angle : 0.535 7.254 26286 Z= 0.282 Chirality : 0.042 0.239 3025 Planarity : 0.004 0.045 3311 Dihedral : 6.544 128.214 2979 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.87 % Allowed : 24.73 % 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: -0.53 (0.17), residues: 2423 helix: 0.98 (0.18), residues: 847 sheet: -1.14 (0.25), residues: 456 loop : -0.99 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.028 0.001 PHE G 192 TYR 0.028 0.001 TYR E 223 ARG 0.008 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 11) link_NAG-ASN : angle 1.79824 ( 33) link_BETA1-4 : bond 0.00137 ( 2) link_BETA1-4 : angle 1.26492 ( 6) hydrogen bonds : bond 0.03836 ( 788) hydrogen bonds : angle 4.51339 ( 2235) SS BOND : bond 0.00271 ( 19) SS BOND : angle 0.60119 ( 38) covalent geometry : bond 0.00325 (19238) covalent geometry : angle 0.53129 (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 310 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 238 time to evaluate : 2.036 Fit side-chains revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8217 (p90) cc_final: 0.8006 (p90) REVERT: B 589 PHE cc_start: 0.8612 (m-80) cc_final: 0.8361 (m-80) REVERT: B 686 ILE cc_start: 0.7379 (pt) cc_final: 0.6967 (mm) REVERT: B 742 TRP cc_start: 0.7643 (t60) cc_final: 0.7403 (t60) REVERT: A 425 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: G 8 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: G 23 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8391 (mt) REVERT: G 46 LYS cc_start: 0.7765 (mttt) cc_final: 0.7486 (mttt) REVERT: G 53 MET cc_start: 0.5437 (mtm) cc_final: 0.4751 (ttt) REVERT: G 142 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7698 (m-10) REVERT: G 244 ASN cc_start: 0.8614 (t0) cc_final: 0.8012 (t0) REVERT: C 44 GLN cc_start: 0.7340 (pp30) cc_final: 0.7127 (pp30) REVERT: C 289 TYR cc_start: 0.8228 (m-80) cc_final: 0.8005 (m-80) REVERT: E 7 SER cc_start: 0.8068 (m) cc_final: 0.7631 (p) REVERT: E 204 ILE cc_start: 0.4014 (OUTLIER) cc_final: 0.3491 (tt) outliers start: 72 outliers final: 53 residues processed: 295 average time/residue: 0.2907 time to fit residues: 132.6733 Evaluate side-chains 284 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 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 812 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 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 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 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 243 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 329 THR 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: 0.9980 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 106 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.096042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081331 restraints weight = 46137.745| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.21 r_work: 0.3291 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1667 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= 0.131 Angle : 0.533 9.463 26286 Z= 0.278 Chirality : 0.043 0.244 3025 Planarity : 0.004 0.045 3311 Dihedral : 6.305 121.086 2979 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.03 % Allowed : 24.78 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2423 helix: 1.04 (0.18), residues: 842 sheet: -1.12 (0.25), residues: 428 loop : -0.97 (0.19), residues: 1153 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 0.030 0.001 PHE G 192 TYR 0.019 0.001 TYR E 223 ARG 0.008 0.000 ARG B 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 11) link_NAG-ASN : angle 1.65723 ( 33) link_BETA1-4 : bond 0.00159 ( 2) link_BETA1-4 : angle 1.25822 ( 6) hydrogen bonds : bond 0.03705 ( 788) hydrogen bonds : angle 4.40735 ( 2235) SS BOND : bond 0.00207 ( 19) SS BOND : angle 0.49032 ( 38) covalent geometry : bond 0.00305 (19238) covalent geometry : angle 0.53036 (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 307 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 2.249 Fit side-chains revert: symmetry clash REVERT: B 589 PHE cc_start: 0.8621 (m-80) cc_final: 0.8372 (m-80) REVERT: B 686 ILE cc_start: 0.7396 (pt) cc_final: 0.6979 (mm) REVERT: A 425 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7979 (m-10) REVERT: G 8 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: G 23 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8401 (mt) REVERT: G 46 LYS cc_start: 0.7824 (mttt) cc_final: 0.7612 (mttt) REVERT: G 53 MET cc_start: 0.5437 (mtm) cc_final: 0.4757 (ttt) REVERT: G 142 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: G 244 ASN cc_start: 0.8584 (t0) cc_final: 0.7986 (t0) REVERT: C 44 GLN cc_start: 0.7328 (pp30) cc_final: 0.7101 (pp30) REVERT: E 7 SER cc_start: 0.8034 (m) cc_final: 0.7627 (p) REVERT: E 204 ILE cc_start: 0.4069 (OUTLIER) cc_final: 0.3542 (tt) REVERT: E 214 VAL cc_start: 0.7842 (m) cc_final: 0.7508 (p) REVERT: E 223 TYR cc_start: 0.7410 (t80) cc_final: 0.7062 (t80) outliers start: 75 outliers final: 61 residues processed: 290 average time/residue: 0.2934 time to fit residues: 133.7482 Evaluate side-chains 293 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 2.358 ------------------------------------------------------------------------------- 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 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 812 LEU 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 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 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 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 71 SER 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: 6.9990 chunk 190 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 0.0980 chunk 195 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.095010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.080223 restraints weight = 46022.270| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.21 r_work: 0.3268 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19270 Z= 0.184 Angle : 0.561 8.301 26286 Z= 0.293 Chirality : 0.044 0.234 3025 Planarity : 0.004 0.046 3311 Dihedral : 6.265 116.921 2979 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.82 % Allowed : 25.11 % Favored : 71.08 % 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: -0.56 (0.17), residues: 2423 helix: 0.93 (0.18), residues: 854 sheet: -1.12 (0.25), residues: 431 loop : -1.03 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 530 HIS 0.007 0.001 HIS E 35 PHE 0.031 0.002 PHE G 192 TYR 0.022 0.001 TYR E 223 ARG 0.008 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 11) link_NAG-ASN : angle 1.72991 ( 33) link_BETA1-4 : bond 0.00125 ( 2) link_BETA1-4 : angle 1.30897 ( 6) hydrogen bonds : bond 0.03980 ( 788) hydrogen bonds : angle 4.49918 ( 2235) SS BOND : bond 0.00238 ( 19) SS BOND : angle 0.55771 ( 38) covalent geometry : bond 0.00431 (19238) covalent geometry : angle 0.55805 (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: 71 poor density : 229 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: B 686 ILE cc_start: 0.7410 (pt) cc_final: 0.6978 (mm) REVERT: A 425 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7998 (m-10) REVERT: G 8 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: G 46 LYS cc_start: 0.7834 (mttt) cc_final: 0.7616 (mttt) REVERT: G 53 MET cc_start: 0.5454 (mtm) cc_final: 0.4769 (ttt) REVERT: G 142 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7736 (m-10) REVERT: G 244 ASN cc_start: 0.8615 (t0) cc_final: 0.7993 (t0) REVERT: C 44 GLN cc_start: 0.7319 (pp30) cc_final: 0.7087 (pp30) REVERT: C 289 TYR cc_start: 0.8232 (m-80) cc_final: 0.8013 (m-80) REVERT: E 7 SER cc_start: 0.8084 (m) cc_final: 0.7649 (p) REVERT: E 204 ILE cc_start: 0.4055 (OUTLIER) cc_final: 0.3544 (tt) REVERT: E 214 VAL cc_start: 0.7844 (m) cc_final: 0.7499 (p) REVERT: E 223 TYR cc_start: 0.7382 (t80) cc_final: 0.7020 (t80) outliers start: 71 outliers final: 63 residues processed: 285 average time/residue: 0.2850 time to fit residues: 127.8442 Evaluate side-chains 292 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 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 812 LEU 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 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 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 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 71 SER 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 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: 3.9990 chunk 187 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 208 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 184 optimal weight: 0.0040 chunk 15 optimal weight: 0.5980 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.094577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079805 restraints weight = 45772.956| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.19 r_work: 0.3259 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19270 Z= 0.198 Angle : 0.573 8.424 26286 Z= 0.301 Chirality : 0.044 0.230 3025 Planarity : 0.004 0.047 3311 Dihedral : 6.189 109.173 2979 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.92 % Allowed : 25.11 % Favored : 70.97 % 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: -0.62 (0.17), residues: 2423 helix: 0.89 (0.18), residues: 854 sheet: -1.18 (0.25), residues: 431 loop : -1.06 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.007 0.001 HIS E 35 PHE 0.032 0.002 PHE G 192 TYR 0.022 0.001 TYR E 223 ARG 0.008 0.000 ARG B 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 11) link_NAG-ASN : angle 1.76277 ( 33) link_BETA1-4 : bond 0.00062 ( 2) link_BETA1-4 : angle 1.35244 ( 6) hydrogen bonds : bond 0.04064 ( 788) hydrogen bonds : angle 4.53492 ( 2235) SS BOND : bond 0.00251 ( 19) SS BOND : angle 0.59409 ( 38) covalent geometry : bond 0.00463 (19238) covalent geometry : angle 0.56982 (26209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12110.56 seconds wall clock time: 209 minutes 52.21 seconds (12592.21 seconds total)