Starting phenix.real_space_refine on Tue Feb 20 11:55:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgq_23328/02_2024/7lgq_23328_neut_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.122 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 P 24 5.49 5 Mg 8 5.21 5 S 96 5.16 5 C 17052 2.51 5 N 4816 2.21 5 O 5320 1.98 5 H 24 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 558": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27340 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6636 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 40, 'TRANS': 827} Chain breaks: 1 Chain: "B" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6636 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 40, 'TRANS': 827} Chain breaks: 1 Chain: "C" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6636 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 40, 'TRANS': 827} Chain breaks: 1 Chain: "D" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6636 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 40, 'TRANS': 827} Chain breaks: 1 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 63 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, 'ASN:plan1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 63 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, 'ASN:plan1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 63 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, 'ASN:plan1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 63 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, 'ASN:plan1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 15.13, per 1000 atoms: 0.55 Number of scatterers: 27340 At special positions: 0 Unit cell: (135.945, 141.075, 147.915, 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) S 96 16.00 P 24 15.00 Mg 8 11.99 O 5320 8.00 N 4816 7.00 C 17052 6.00 H 24 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.08 Conformation dependent library (CDL) restraints added in 4.8 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 24 sheets defined 33.5% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.923A pdb=" N VAL A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 137 removed outlier: 3.590A pdb=" N VAL A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 3.661A pdb=" N GLU A 148 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS A 149 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 158 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.575A pdb=" N ALA A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 4.602A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 removed outlier: 4.138A pdb=" N GLU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.761A pdb=" N GLN A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 441 through 444 No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 458 through 461 No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.743A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.639A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.842A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 595 through 608 removed outlier: 3.651A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 removed outlier: 3.876A pdb=" N ALA A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASP A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 622 through 629' Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.676A pdb=" N ARG A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'A' and resid 750 through 761 removed outlier: 3.843A pdb=" N ALA A 755 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 756 " --> pdb=" O TYR A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 791 removed outlier: 3.993A pdb=" N GLN A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.810A pdb=" N GLU A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 867 removed outlier: 4.199A pdb=" N LYS A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.923A pdb=" N VAL B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 137 removed outlier: 3.591A pdb=" N VAL B 137 " --> pdb=" O CYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 removed outlier: 3.661A pdb=" N GLU B 148 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS B 149 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 158 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 220 through 230 removed outlier: 3.576A pdb=" N ALA B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 4.602A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 removed outlier: 4.137A pdb=" N GLU B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.761A pdb=" N GLN B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 410 through 422 Processing helix chain 'B' and resid 441 through 444 No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 458 through 461 No H-bonds generated for 'chain 'B' and resid 458 through 461' Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.743A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 513 removed outlier: 3.638A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.842A pdb=" N VAL B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 595 through 608 removed outlier: 3.651A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 629 removed outlier: 3.876A pdb=" N ALA B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA B 628 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASP B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 622 through 629' Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.676A pdb=" N ARG B 653 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 691 through 706 Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.843A pdb=" N ALA B 755 " --> pdb=" O GLY B 752 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 756 " --> pdb=" O TYR B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 791 removed outlier: 3.994A pdb=" N GLN B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.810A pdb=" N GLU B 823 " --> pdb=" O GLY B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 867 removed outlier: 4.199A pdb=" N LYS B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.923A pdb=" N VAL C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 137 removed outlier: 3.590A pdb=" N VAL C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 3.661A pdb=" N GLU C 148 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS C 149 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 158 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.575A pdb=" N ALA C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 253 removed outlier: 4.602A pdb=" N ASN C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 4.138A pdb=" N GLU C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.760A pdb=" N GLN C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 410 through 422 Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 458 through 461 No H-bonds generated for 'chain 'C' and resid 458 through 461' Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.743A pdb=" N MET C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 513 removed outlier: 3.639A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.842A pdb=" N VAL C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 595 through 608 removed outlier: 3.651A pdb=" N LYS C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.502A pdb=" N ASP C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.676A pdb=" N ARG C 653 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 691 through 706 Processing helix chain 'C' and resid 711 through 720 Processing helix chain 'C' and resid 750 through 761 removed outlier: 3.843A pdb=" N ALA C 755 " --> pdb=" O GLY C 752 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 756 " --> pdb=" O TYR C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 791 removed outlier: 3.994A pdb=" N GLN C 791 " --> pdb=" O GLN C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 823 removed outlier: 3.810A pdb=" N GLU C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 867 removed outlier: 4.199A pdb=" N LYS C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 80 through 92 removed outlier: 3.923A pdb=" N VAL D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 137 removed outlier: 3.590A pdb=" N VAL D 137 " --> pdb=" O CYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 removed outlier: 3.661A pdb=" N GLU D 148 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 158 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.576A pdb=" N ALA D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 253 removed outlier: 4.602A pdb=" N ASN D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 290 removed outlier: 4.138A pdb=" N GLU D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.761A pdb=" N GLN D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 410 through 422 Processing helix chain 'D' and resid 441 through 444 No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 458 through 461 No H-bonds generated for 'chain 'D' and resid 458 through 461' Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.743A pdb=" N MET D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 513 removed outlier: 3.639A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 removed outlier: 3.842A pdb=" N VAL D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 595 through 608 removed outlier: 3.651A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.502A pdb=" N ASP D 629 " --> pdb=" O ALA D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.676A pdb=" N ARG D 653 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 691 through 706 Processing helix chain 'D' and resid 711 through 719 Processing helix chain 'D' and resid 750 through 761 removed outlier: 3.843A pdb=" N ALA D 755 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 756 " --> pdb=" O TYR D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 791 removed outlier: 3.994A pdb=" N GLN D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.810A pdb=" N GLU D 823 " --> pdb=" O GLY D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 867 removed outlier: 4.200A pdb=" N LYS D 867 " --> pdb=" O ILE D 863 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 99 through 104 removed outlier: 4.272A pdb=" N VAL A 109 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= C, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.751A pdb=" N LEU A 311 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 320 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG A 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU A 322 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP A 307 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= E, first strand: chain 'A' and resid 672 through 678 removed outlier: 6.794A pdb=" N LEU A 665 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A 635 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 527 " --> pdb=" O CYS A 531 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N CYS A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 733 through 736 Processing sheet with id= G, first strand: chain 'B' and resid 99 through 104 removed outlier: 4.272A pdb=" N VAL B 109 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= I, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.751A pdb=" N LEU B 311 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 320 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG B 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU B 322 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP B 307 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 327 through 329 Processing sheet with id= K, first strand: chain 'B' and resid 672 through 678 removed outlier: 6.793A pdb=" N LEU B 665 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL B 635 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 527 " --> pdb=" O CYS B 531 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N CYS B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 733 through 736 Processing sheet with id= M, first strand: chain 'C' and resid 99 through 104 removed outlier: 4.272A pdb=" N VAL C 109 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'C' and resid 400 through 403 removed outlier: 6.751A pdb=" N LEU C 311 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL C 320 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG C 309 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU C 322 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP C 307 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= Q, first strand: chain 'C' and resid 672 through 678 removed outlier: 6.794A pdb=" N LEU C 665 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL C 635 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 527 " --> pdb=" O CYS C 531 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 733 through 736 Processing sheet with id= S, first strand: chain 'D' and resid 99 through 104 removed outlier: 4.273A pdb=" N VAL D 109 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= U, first strand: chain 'D' and resid 400 through 403 removed outlier: 6.750A pdb=" N LEU D 311 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL D 320 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG D 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU D 322 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP D 307 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 327 through 329 Processing sheet with id= W, first strand: chain 'D' and resid 672 through 678 removed outlier: 6.794A pdb=" N LEU D 665 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL D 635 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 527 " --> pdb=" O CYS D 531 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N CYS D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 733 through 736 935 hydrogen bonds defined for protein. 2487 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: 10.79 Time building geometry restraints manager: 11.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 24 1.05 - 1.24: 4518 1.24 - 1.43: 6941 1.43 - 1.63: 16137 1.63 - 1.82: 172 Bond restraints: 27792 Sorted by residual: bond pdb=" C 7ID G 5 " pdb=" N 7ID G 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID H 5 " pdb=" N 7ID H 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID F 5 " pdb=" N 7ID F 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID E 5 " pdb=" N 7ID E 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID E 6 " pdb=" N 7ID E 7 " ideal model delta sigma weight residual 1.329 1.479 -0.150 1.40e-02 5.10e+03 1.15e+02 ... (remaining 27787 not shown) Histogram of bond angle deviations from ideal: 97.04 - 106.41: 1163 106.41 - 115.78: 16814 115.78 - 125.16: 19129 125.16 - 134.53: 698 134.53 - 143.91: 12 Bond angle restraints: 37816 Sorted by residual: angle pdb=" PB ATP C 902 " pdb=" O3B ATP C 902 " pdb=" PG ATP C 902 " ideal model delta sigma weight residual 139.87 129.17 10.70 1.00e+00 1.00e+00 1.15e+02 angle pdb=" PB ATP D 902 " pdb=" O3B ATP D 902 " pdb=" PG ATP D 902 " ideal model delta sigma weight residual 139.87 129.17 10.70 1.00e+00 1.00e+00 1.15e+02 angle pdb=" PB ATP A 902 " pdb=" O3B ATP A 902 " pdb=" PG ATP A 902 " ideal model delta sigma weight residual 139.87 129.20 10.67 1.00e+00 1.00e+00 1.14e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 129.22 10.65 1.00e+00 1.00e+00 1.14e+02 angle pdb=" C GLY C 773 " pdb=" N PRO C 774 " pdb=" CA PRO C 774 " ideal model delta sigma weight residual 119.92 130.40 -10.48 1.07e+00 8.73e-01 9.58e+01 ... (remaining 37811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 16456 32.42 - 64.83: 334 64.83 - 97.25: 82 97.25 - 129.66: 20 129.66 - 162.08: 12 Dihedral angle restraints: 16904 sinusoidal: 6932 harmonic: 9972 Sorted by residual: dihedral pdb=" C ALA C 790 " pdb=" N ALA C 790 " pdb=" CA ALA C 790 " pdb=" CB ALA C 790 " ideal model delta harmonic sigma weight residual -122.60 -154.45 31.85 0 2.50e+00 1.60e-01 1.62e+02 dihedral pdb=" C ALA D 790 " pdb=" N ALA D 790 " pdb=" CA ALA D 790 " pdb=" CB ALA D 790 " ideal model delta harmonic sigma weight residual -122.60 -154.45 31.85 0 2.50e+00 1.60e-01 1.62e+02 dihedral pdb=" C ALA B 790 " pdb=" N ALA B 790 " pdb=" CA ALA B 790 " pdb=" CB ALA B 790 " ideal model delta harmonic sigma weight residual -122.60 -154.44 31.84 0 2.50e+00 1.60e-01 1.62e+02 ... (remaining 16901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 4280 0.265 - 0.530: 60 0.530 - 0.795: 0 0.795 - 1.059: 0 1.059 - 1.324: 8 Chirality restraints: 4348 Sorted by residual: chirality pdb=" CA ALA C 790 " pdb=" N ALA C 790 " pdb=" C ALA C 790 " pdb=" CB ALA C 790 " both_signs ideal model delta sigma weight residual False 2.48 1.16 1.32 2.00e-01 2.50e+01 4.38e+01 chirality pdb=" CA ALA B 790 " pdb=" N ALA B 790 " pdb=" C ALA B 790 " pdb=" CB ALA B 790 " both_signs ideal model delta sigma weight residual False 2.48 1.16 1.32 2.00e-01 2.50e+01 4.38e+01 chirality pdb=" CA ALA D 790 " pdb=" N ALA D 790 " pdb=" C ALA D 790 " pdb=" CB ALA D 790 " both_signs ideal model delta sigma weight residual False 2.48 1.16 1.32 2.00e-01 2.50e+01 4.38e+01 ... (remaining 4345 not shown) Planarity restraints: 4932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 747 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ALA C 747 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA C 747 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS C 748 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 747 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA D 747 " -0.062 2.00e-02 2.50e+03 pdb=" O ALA D 747 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS D 748 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 747 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA A 747 " -0.062 2.00e-02 2.50e+03 pdb=" O ALA A 747 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS A 748 " 0.021 2.00e-02 2.50e+03 ... (remaining 4929 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.36: 24 2.36 - 2.92: 11687 2.92 - 3.48: 29464 3.48 - 4.04: 50949 4.04 - 4.60: 72615 Nonbonded interactions: 164739 Sorted by model distance: nonbonded pdb=" OE2 GLU A 558 " pdb="MG MG A 903 " model vdw 1.806 2.050 nonbonded pdb=" OE2 GLU B 558 " pdb="MG MG B 903 " model vdw 1.806 2.050 nonbonded pdb=" OE2 GLU D 558 " pdb="MG MG D 903 " model vdw 1.806 2.050 nonbonded pdb=" OE2 GLU C 558 " pdb="MG MG C 903 " model vdw 1.806 2.050 nonbonded pdb=" OG1 THR D 500 " pdb="MG MG D 903 " model vdw 2.020 2.050 ... (remaining 164734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.580 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: 0.690 Extract box with map and model: 15.050 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 75.710 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.290 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.022 0.211 27768 Z= 1.452 Angle : 1.909 21.175 37764 Z= 1.247 Chirality : 0.112 1.324 4348 Planarity : 0.009 0.036 4928 Dihedral : 15.215 162.077 10528 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.16 % Cbeta Deviations : 0.75 % 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: -0.63 (0.13), residues: 3456 helix: -1.07 (0.13), residues: 1256 sheet: 1.22 (0.21), residues: 584 loop : -0.35 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP C 181 HIS 0.019 0.004 HIS D 586 PHE 0.028 0.005 PHE D 58 TYR 0.043 0.007 TYR B 829 ARG 0.008 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 382 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6574 (pmt170) REVERT: A 316 LYS cc_start: 0.8739 (tttt) cc_final: 0.8075 (mtmm) REVERT: A 342 LYS cc_start: 0.7020 (tttm) cc_final: 0.6553 (mttm) REVERT: A 445 ASN cc_start: 0.8029 (t0) cc_final: 0.7735 (t160) REVERT: A 534 LYS cc_start: 0.7740 (mttt) cc_final: 0.7420 (mttt) REVERT: A 589 LEU cc_start: 0.6020 (mt) cc_final: 0.5760 (mp) REVERT: A 600 LYS cc_start: 0.7375 (mttt) cc_final: 0.7135 (mmtm) REVERT: A 630 LYS cc_start: 0.7105 (mmtt) cc_final: 0.6684 (mtpt) REVERT: A 661 GLU cc_start: 0.7724 (pt0) cc_final: 0.7004 (pp20) REVERT: A 712 GLU cc_start: 0.7161 (tp30) cc_final: 0.6708 (mp0) REVERT: B 18 ARG cc_start: 0.7387 (mtt180) cc_final: 0.6510 (pmt170) REVERT: B 316 LYS cc_start: 0.8738 (tttt) cc_final: 0.8074 (mtmm) REVERT: B 342 LYS cc_start: 0.6977 (tttm) cc_final: 0.6551 (mttm) REVERT: B 442 ARG cc_start: 0.8312 (ptt-90) cc_final: 0.8106 (ttp-110) REVERT: B 445 ASN cc_start: 0.8005 (t0) cc_final: 0.7690 (t160) REVERT: B 534 LYS cc_start: 0.7752 (mttt) cc_final: 0.7428 (mttt) REVERT: B 600 LYS cc_start: 0.7494 (mttt) cc_final: 0.7223 (mmtm) REVERT: B 630 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6781 (mtpt) REVERT: B 661 GLU cc_start: 0.7770 (pt0) cc_final: 0.7094 (pp20) REVERT: B 669 GLU cc_start: 0.7768 (tt0) cc_final: 0.7374 (tp30) REVERT: C 18 ARG cc_start: 0.7454 (mtt180) cc_final: 0.6616 (pmt170) REVERT: C 316 LYS cc_start: 0.8711 (tttt) cc_final: 0.7990 (mtmm) REVERT: C 342 LYS cc_start: 0.7056 (tttm) cc_final: 0.6628 (mttm) REVERT: C 372 ARG cc_start: 0.5702 (mtt90) cc_final: 0.5266 (ttt180) REVERT: C 445 ASN cc_start: 0.7982 (t0) cc_final: 0.7672 (t160) REVERT: C 534 LYS cc_start: 0.7803 (mttt) cc_final: 0.7474 (mttt) REVERT: C 600 LYS cc_start: 0.7450 (mttt) cc_final: 0.7200 (mmtm) REVERT: C 630 LYS cc_start: 0.7093 (mmtt) cc_final: 0.6727 (mtpt) REVERT: C 661 GLU cc_start: 0.7750 (pt0) cc_final: 0.7008 (pp20) REVERT: D 18 ARG cc_start: 0.7471 (mtt180) cc_final: 0.6609 (pmt170) REVERT: D 316 LYS cc_start: 0.8719 (tttt) cc_final: 0.8056 (mtmm) REVERT: D 342 LYS cc_start: 0.7053 (tttm) cc_final: 0.6626 (mttm) REVERT: D 371 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6785 (tp30) REVERT: D 372 ARG cc_start: 0.5716 (mtt90) cc_final: 0.5259 (ttt180) REVERT: D 445 ASN cc_start: 0.7997 (t0) cc_final: 0.7716 (t160) REVERT: D 534 LYS cc_start: 0.7715 (mttt) cc_final: 0.7384 (mttt) REVERT: D 600 LYS cc_start: 0.7417 (mttt) cc_final: 0.7141 (mmtm) REVERT: D 630 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6776 (mtpt) REVERT: D 661 GLU cc_start: 0.7792 (pt0) cc_final: 0.7055 (pp20) REVERT: D 712 GLU cc_start: 0.7147 (tp30) cc_final: 0.6642 (mp0) outliers start: 8 outliers final: 0 residues processed: 390 average time/residue: 1.6533 time to fit residues: 732.9345 Evaluate side-chains 257 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 0.7980 chunk 260 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 312 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 541 GLN A 748 HIS B 202 GLN B 541 GLN B 748 HIS C 202 GLN C 541 GLN C 748 HIS ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN D 748 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27768 Z= 0.188 Angle : 0.589 6.071 37764 Z= 0.323 Chirality : 0.044 0.153 4348 Planarity : 0.004 0.034 4928 Dihedral : 17.111 175.390 4308 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.41 % Allowed : 5.06 % Favored : 93.53 % 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: -0.26 (0.14), residues: 3456 helix: -0.02 (0.14), residues: 1312 sheet: 0.63 (0.21), residues: 640 loop : -0.55 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 278 HIS 0.007 0.001 HIS A 83 PHE 0.010 0.001 PHE A 58 TYR 0.012 0.001 TYR A 519 ARG 0.003 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 274 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6425 (pmt170) REVERT: A 35 ARG cc_start: 0.5786 (mtm180) cc_final: 0.5556 (mtp-110) REVERT: A 173 GLU cc_start: 0.8104 (tp30) cc_final: 0.7900 (tp30) REVERT: A 316 LYS cc_start: 0.8653 (tttt) cc_final: 0.8137 (mtmm) REVERT: A 534 LYS cc_start: 0.7651 (mttt) cc_final: 0.7395 (mttt) REVERT: A 589 LEU cc_start: 0.6287 (mt) cc_final: 0.6046 (mp) REVERT: A 600 LYS cc_start: 0.7228 (mttt) cc_final: 0.7018 (mmtm) REVERT: A 630 LYS cc_start: 0.7204 (mmtt) cc_final: 0.6801 (mtpt) REVERT: A 661 GLU cc_start: 0.7698 (pt0) cc_final: 0.6968 (pp20) REVERT: A 712 GLU cc_start: 0.6878 (tp30) cc_final: 0.6597 (mp0) REVERT: B 18 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6424 (pmt170) REVERT: B 173 GLU cc_start: 0.8111 (tp30) cc_final: 0.7908 (tp30) REVERT: B 316 LYS cc_start: 0.8653 (tttt) cc_final: 0.8125 (mtmm) REVERT: B 342 LYS cc_start: 0.7061 (tttm) cc_final: 0.6437 (mttm) REVERT: B 534 LYS cc_start: 0.7673 (mttt) cc_final: 0.7390 (mttt) REVERT: B 600 LYS cc_start: 0.7358 (mttt) cc_final: 0.7157 (mmtm) REVERT: B 630 LYS cc_start: 0.7213 (mmtt) cc_final: 0.6822 (mtpt) REVERT: B 661 GLU cc_start: 0.7721 (pt0) cc_final: 0.7005 (pp20) REVERT: B 712 GLU cc_start: 0.6801 (tp30) cc_final: 0.6547 (mp0) REVERT: C 18 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6432 (pmt170) REVERT: C 173 GLU cc_start: 0.8116 (tp30) cc_final: 0.7915 (tp30) REVERT: C 316 LYS cc_start: 0.8658 (tttt) cc_final: 0.8122 (mtmm) REVERT: C 534 LYS cc_start: 0.7728 (mttt) cc_final: 0.7450 (mttt) REVERT: C 630 LYS cc_start: 0.7197 (mmtt) cc_final: 0.6835 (mtpt) REVERT: C 661 GLU cc_start: 0.7721 (pt0) cc_final: 0.6974 (pp20) REVERT: C 712 GLU cc_start: 0.6743 (tp30) cc_final: 0.6537 (mp0) REVERT: D 18 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6425 (pmt170) REVERT: D 35 ARG cc_start: 0.5617 (mtm180) cc_final: 0.5386 (mtp-110) REVERT: D 173 GLU cc_start: 0.8107 (tp30) cc_final: 0.7903 (tp30) REVERT: D 316 LYS cc_start: 0.8657 (tttt) cc_final: 0.8130 (mtmm) REVERT: D 445 ASN cc_start: 0.7986 (t0) cc_final: 0.7785 (t160) REVERT: D 534 LYS cc_start: 0.7619 (mttt) cc_final: 0.7333 (mttt) REVERT: D 630 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6877 (mtpt) REVERT: D 661 GLU cc_start: 0.7718 (pt0) cc_final: 0.6966 (pp20) REVERT: D 712 GLU cc_start: 0.6852 (tp30) cc_final: 0.6576 (mp0) outliers start: 40 outliers final: 15 residues processed: 305 average time/residue: 1.6441 time to fit residues: 571.3945 Evaluate side-chains 251 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 632 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 338 optimal weight: 20.0000 chunk 278 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 445 ASN C 445 ASN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 27768 Z= 0.396 Angle : 0.664 6.322 37764 Z= 0.353 Chirality : 0.048 0.170 4348 Planarity : 0.005 0.055 4928 Dihedral : 15.946 158.502 4308 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.32 % Allowed : 6.01 % Favored : 91.67 % 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: -0.57 (0.14), residues: 3456 helix: -0.14 (0.14), residues: 1316 sheet: 0.47 (0.21), residues: 596 loop : -0.82 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 278 HIS 0.011 0.002 HIS B 586 PHE 0.022 0.002 PHE A 58 TYR 0.018 0.002 TYR A 530 ARG 0.008 0.001 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 258 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7371 (tttt) cc_final: 0.6934 (ttpp) REVERT: A 18 ARG cc_start: 0.7435 (mtt180) cc_final: 0.6573 (pmt170) REVERT: A 134 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.5041 (ttt90) REVERT: A 304 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8168 (mm-30) REVERT: A 316 LYS cc_start: 0.8819 (tttt) cc_final: 0.8233 (mtmm) REVERT: A 372 ARG cc_start: 0.5663 (ttm-80) cc_final: 0.4909 (ttt180) REVERT: A 534 LYS cc_start: 0.7914 (mttt) cc_final: 0.7556 (mttt) REVERT: A 558 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8274 (pt0) REVERT: A 600 LYS cc_start: 0.7407 (mttt) cc_final: 0.7179 (mmtm) REVERT: A 630 LYS cc_start: 0.7285 (mmtt) cc_final: 0.6843 (mtpt) REVERT: A 654 ASN cc_start: 0.7091 (m-40) cc_final: 0.6847 (m110) REVERT: A 661 GLU cc_start: 0.7842 (pt0) cc_final: 0.6856 (pp20) REVERT: A 712 GLU cc_start: 0.6940 (tp30) cc_final: 0.6605 (mp0) REVERT: B 5 LYS cc_start: 0.7294 (tttt) cc_final: 0.7043 (ttmm) REVERT: B 18 ARG cc_start: 0.7431 (mtt180) cc_final: 0.6570 (pmt170) REVERT: B 134 ARG cc_start: 0.5326 (OUTLIER) cc_final: 0.5016 (ttt90) REVERT: B 173 GLU cc_start: 0.8148 (tp30) cc_final: 0.7945 (tp30) REVERT: B 304 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8165 (mm-30) REVERT: B 316 LYS cc_start: 0.8823 (tttt) cc_final: 0.8242 (mtmm) REVERT: B 342 LYS cc_start: 0.7171 (tttm) cc_final: 0.6570 (mttm) REVERT: B 372 ARG cc_start: 0.5655 (ttm-80) cc_final: 0.4911 (ttt180) REVERT: B 534 LYS cc_start: 0.7918 (mttt) cc_final: 0.7621 (mttm) REVERT: B 558 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: B 600 LYS cc_start: 0.7432 (mttt) cc_final: 0.7210 (mmtm) REVERT: B 630 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6825 (mtpt) REVERT: B 654 ASN cc_start: 0.6999 (m-40) cc_final: 0.6757 (m110) REVERT: B 661 GLU cc_start: 0.7852 (pt0) cc_final: 0.6872 (pp20) REVERT: B 712 GLU cc_start: 0.6933 (tp30) cc_final: 0.6605 (mp0) REVERT: C 5 LYS cc_start: 0.7326 (tttt) cc_final: 0.7075 (ttmm) REVERT: C 18 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6531 (pmt170) REVERT: C 304 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8151 (mm-30) REVERT: C 316 LYS cc_start: 0.8825 (tttt) cc_final: 0.8244 (mtmm) REVERT: C 534 LYS cc_start: 0.7921 (mttt) cc_final: 0.7626 (mttm) REVERT: C 558 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: C 630 LYS cc_start: 0.7291 (mmtt) cc_final: 0.6877 (mtpt) REVERT: C 654 ASN cc_start: 0.7092 (m-40) cc_final: 0.6851 (m110) REVERT: C 661 GLU cc_start: 0.7845 (pt0) cc_final: 0.6855 (pp20) REVERT: C 836 THR cc_start: 0.2665 (OUTLIER) cc_final: 0.2464 (m) REVERT: D 5 LYS cc_start: 0.7326 (tttt) cc_final: 0.7075 (ttmm) REVERT: D 18 ARG cc_start: 0.7402 (mtt180) cc_final: 0.6530 (pmt170) REVERT: D 173 GLU cc_start: 0.8150 (tp30) cc_final: 0.7948 (tp30) REVERT: D 304 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8149 (mm-30) REVERT: D 316 LYS cc_start: 0.8822 (tttt) cc_final: 0.8240 (mtmm) REVERT: D 534 LYS cc_start: 0.7925 (mttt) cc_final: 0.7626 (mttm) REVERT: D 558 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: D 630 LYS cc_start: 0.7305 (mmtt) cc_final: 0.6881 (mtpt) REVERT: D 654 ASN cc_start: 0.7092 (m-40) cc_final: 0.6848 (m110) REVERT: D 661 GLU cc_start: 0.7844 (pt0) cc_final: 0.6871 (pp20) REVERT: D 712 GLU cc_start: 0.6934 (tp30) cc_final: 0.6601 (mp0) REVERT: D 836 THR cc_start: 0.2806 (OUTLIER) cc_final: 0.2578 (m) outliers start: 66 outliers final: 28 residues processed: 302 average time/residue: 1.6064 time to fit residues: 554.8098 Evaluate side-chains 272 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 314 optimal weight: 2.9990 chunk 332 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 452 ASN B 327 HIS B 452 ASN C 327 HIS C 452 ASN D 202 GLN D 327 HIS D 452 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 27768 Z= 0.316 Angle : 0.564 6.237 37764 Z= 0.302 Chirality : 0.046 0.149 4348 Planarity : 0.004 0.042 4928 Dihedral : 14.638 123.225 4308 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.04 % Allowed : 6.93 % Favored : 91.03 % 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: -0.73 (0.14), residues: 3456 helix: -0.13 (0.14), residues: 1320 sheet: 0.19 (0.21), residues: 608 loop : -0.98 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 278 HIS 0.008 0.002 HIS C 586 PHE 0.018 0.002 PHE A 58 TYR 0.016 0.002 TYR C 519 ARG 0.005 0.001 ARG D 511 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 253 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7420 (tttt) cc_final: 0.6981 (ttpp) REVERT: A 18 ARG cc_start: 0.7498 (mtt180) cc_final: 0.6629 (pmt170) REVERT: A 134 ARG cc_start: 0.5335 (OUTLIER) cc_final: 0.5070 (ttt90) REVERT: A 304 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8161 (mm-30) REVERT: A 316 LYS cc_start: 0.8757 (tttt) cc_final: 0.8300 (mtmm) REVERT: A 372 ARG cc_start: 0.5676 (ttm-80) cc_final: 0.4908 (ttt180) REVERT: A 445 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.8041 (t0) REVERT: A 534 LYS cc_start: 0.7847 (mttt) cc_final: 0.7550 (mttm) REVERT: A 558 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: A 600 LYS cc_start: 0.7348 (mttt) cc_final: 0.7146 (mmtm) REVERT: A 630 LYS cc_start: 0.7366 (mmtt) cc_final: 0.6825 (mtmt) REVERT: A 654 ASN cc_start: 0.7078 (m-40) cc_final: 0.6843 (m110) REVERT: A 661 GLU cc_start: 0.7909 (pt0) cc_final: 0.6935 (pp20) REVERT: B 5 LYS cc_start: 0.7389 (tttt) cc_final: 0.6966 (ttpp) REVERT: B 18 ARG cc_start: 0.7490 (mtt180) cc_final: 0.6621 (pmt170) REVERT: B 134 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.4983 (ttt90) REVERT: B 304 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8153 (mm-30) REVERT: B 316 LYS cc_start: 0.8767 (tttt) cc_final: 0.8305 (mtmm) REVERT: B 372 ARG cc_start: 0.5691 (ttm-80) cc_final: 0.4906 (ttt180) REVERT: B 445 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.8025 (t0) REVERT: B 534 LYS cc_start: 0.7845 (mttt) cc_final: 0.7547 (mttm) REVERT: B 558 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8252 (pt0) REVERT: B 600 LYS cc_start: 0.7377 (mttt) cc_final: 0.7156 (mmtm) REVERT: B 630 LYS cc_start: 0.7357 (mmtt) cc_final: 0.6808 (mtmt) REVERT: B 654 ASN cc_start: 0.7080 (m-40) cc_final: 0.6832 (m110) REVERT: B 661 GLU cc_start: 0.7892 (pt0) cc_final: 0.6930 (pp20) REVERT: C 5 LYS cc_start: 0.7400 (tttt) cc_final: 0.6975 (ttpp) REVERT: C 18 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6620 (pmt170) REVERT: C 304 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8161 (mm-30) REVERT: C 316 LYS cc_start: 0.8753 (tttt) cc_final: 0.8305 (mtmm) REVERT: C 372 ARG cc_start: 0.5746 (ttm-80) cc_final: 0.4958 (ttt180) REVERT: C 534 LYS cc_start: 0.7836 (mttt) cc_final: 0.7540 (mttm) REVERT: C 558 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: C 630 LYS cc_start: 0.7334 (mmtt) cc_final: 0.6828 (mtmt) REVERT: C 654 ASN cc_start: 0.7081 (m-40) cc_final: 0.6849 (m110) REVERT: C 661 GLU cc_start: 0.7933 (pt0) cc_final: 0.6944 (pp20) REVERT: D 5 LYS cc_start: 0.7400 (tttt) cc_final: 0.6975 (ttpp) REVERT: D 18 ARG cc_start: 0.7487 (mtt180) cc_final: 0.6618 (pmt170) REVERT: D 35 ARG cc_start: 0.5628 (mtp-110) cc_final: 0.5399 (mtp-110) REVERT: D 304 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8160 (mm-30) REVERT: D 316 LYS cc_start: 0.8773 (tttt) cc_final: 0.8320 (mtmm) REVERT: D 534 LYS cc_start: 0.7832 (mttt) cc_final: 0.7533 (mttm) REVERT: D 558 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: D 630 LYS cc_start: 0.7330 (mmtt) cc_final: 0.6849 (mtmt) REVERT: D 654 ASN cc_start: 0.7093 (m-40) cc_final: 0.6862 (m110) REVERT: D 661 GLU cc_start: 0.7897 (pt0) cc_final: 0.6930 (pp20) outliers start: 58 outliers final: 33 residues processed: 291 average time/residue: 1.6939 time to fit residues: 561.1698 Evaluate side-chains 277 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 236 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 677 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 283 optimal weight: 0.5980 chunk 229 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 ASN B 707 ASN C 445 ASN C 707 ASN D 445 ASN D 707 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 27768 Z= 0.254 Angle : 0.508 6.199 37764 Z= 0.272 Chirality : 0.044 0.145 4348 Planarity : 0.004 0.039 4928 Dihedral : 13.558 111.315 4308 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.07 % Allowed : 7.59 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3456 helix: -0.08 (0.14), residues: 1364 sheet: 0.02 (0.20), residues: 668 loop : -0.98 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 278 HIS 0.006 0.001 HIS D 586 PHE 0.013 0.001 PHE A 58 TYR 0.016 0.002 TYR C 116 ARG 0.003 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 256 time to evaluate : 3.273 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7404 (tttt) cc_final: 0.6953 (ttpp) REVERT: A 18 ARG cc_start: 0.7509 (mtt180) cc_final: 0.6640 (pmt170) REVERT: A 134 ARG cc_start: 0.5308 (OUTLIER) cc_final: 0.5065 (ttt90) REVERT: A 304 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8171 (mm-30) REVERT: A 316 LYS cc_start: 0.8707 (tttt) cc_final: 0.8258 (mtmm) REVERT: A 355 ASN cc_start: 0.6445 (m110) cc_final: 0.6062 (m-40) REVERT: A 534 LYS cc_start: 0.7769 (mttt) cc_final: 0.7454 (mttm) REVERT: A 558 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: A 630 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6802 (mtmt) REVERT: A 654 ASN cc_start: 0.7077 (m-40) cc_final: 0.6850 (m110) REVERT: A 661 GLU cc_start: 0.7910 (pt0) cc_final: 0.6961 (pp20) REVERT: A 712 GLU cc_start: 0.6868 (tp30) cc_final: 0.6576 (mp0) REVERT: B 5 LYS cc_start: 0.7405 (tttt) cc_final: 0.6951 (ttpp) REVERT: B 18 ARG cc_start: 0.7506 (mtt180) cc_final: 0.6636 (pmt170) REVERT: B 134 ARG cc_start: 0.5285 (OUTLIER) cc_final: 0.4987 (ttt90) REVERT: B 304 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8163 (mm-30) REVERT: B 316 LYS cc_start: 0.8714 (tttt) cc_final: 0.8255 (mtmm) REVERT: B 355 ASN cc_start: 0.6446 (m110) cc_final: 0.5892 (t0) REVERT: B 534 LYS cc_start: 0.7773 (mttt) cc_final: 0.7457 (mttm) REVERT: B 558 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: B 630 LYS cc_start: 0.7377 (mmtt) cc_final: 0.6843 (mtmt) REVERT: B 654 ASN cc_start: 0.7058 (m-40) cc_final: 0.6832 (m110) REVERT: B 661 GLU cc_start: 0.7930 (pt0) cc_final: 0.6984 (pp20) REVERT: B 712 GLU cc_start: 0.6864 (tp30) cc_final: 0.6574 (mp0) REVERT: C 5 LYS cc_start: 0.7411 (tttt) cc_final: 0.6968 (ttpp) REVERT: C 18 ARG cc_start: 0.7501 (mtt180) cc_final: 0.6635 (pmt170) REVERT: C 304 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8167 (mm-30) REVERT: C 316 LYS cc_start: 0.8710 (tttt) cc_final: 0.8251 (mtmm) REVERT: C 355 ASN cc_start: 0.6511 (m110) cc_final: 0.6148 (m-40) REVERT: C 372 ARG cc_start: 0.5747 (ttm-80) cc_final: 0.4956 (ttt180) REVERT: C 534 LYS cc_start: 0.7773 (mttt) cc_final: 0.7458 (mttm) REVERT: C 558 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: C 630 LYS cc_start: 0.7360 (mmtt) cc_final: 0.6849 (mtmt) REVERT: C 654 ASN cc_start: 0.7058 (m-40) cc_final: 0.6833 (m110) REVERT: C 661 GLU cc_start: 0.7906 (pt0) cc_final: 0.6956 (pp20) REVERT: C 836 THR cc_start: 0.2711 (OUTLIER) cc_final: 0.2468 (m) REVERT: D 5 LYS cc_start: 0.7409 (tttt) cc_final: 0.6965 (ttpp) REVERT: D 18 ARG cc_start: 0.7500 (mtt180) cc_final: 0.6633 (pmt170) REVERT: D 35 ARG cc_start: 0.5637 (mtp-110) cc_final: 0.5405 (mtp-110) REVERT: D 304 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8165 (mm-30) REVERT: D 316 LYS cc_start: 0.8706 (tttt) cc_final: 0.8247 (mtmm) REVERT: D 355 ASN cc_start: 0.6457 (m110) cc_final: 0.6091 (m-40) REVERT: D 534 LYS cc_start: 0.7773 (mttt) cc_final: 0.7457 (mttm) REVERT: D 558 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: D 630 LYS cc_start: 0.7374 (mmtt) cc_final: 0.6862 (mtmt) REVERT: D 654 ASN cc_start: 0.7080 (m-40) cc_final: 0.6855 (m110) REVERT: D 661 GLU cc_start: 0.7923 (pt0) cc_final: 0.6968 (pp20) REVERT: D 712 GLU cc_start: 0.6865 (tp30) cc_final: 0.6574 (mp0) REVERT: D 836 THR cc_start: 0.2689 (OUTLIER) cc_final: 0.2444 (m) outliers start: 59 outliers final: 37 residues processed: 296 average time/residue: 1.7057 time to fit residues: 579.1422 Evaluate side-chains 285 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 240 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 0.4980 chunk 299 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 332 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 707 ASN D 191 GLN D 707 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 27768 Z= 0.192 Angle : 0.471 6.193 37764 Z= 0.251 Chirality : 0.043 0.143 4348 Planarity : 0.003 0.038 4928 Dihedral : 13.076 109.212 4308 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.62 % Allowed : 8.23 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3456 helix: 0.12 (0.15), residues: 1360 sheet: 0.02 (0.20), residues: 668 loop : -0.97 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 278 HIS 0.004 0.001 HIS B 586 PHE 0.012 0.001 PHE C 638 TYR 0.015 0.001 TYR C 116 ARG 0.002 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 253 time to evaluate : 3.075 Fit side-chains REVERT: A 5 LYS cc_start: 0.7299 (tttt) cc_final: 0.6919 (ttpp) REVERT: A 18 ARG cc_start: 0.7519 (mtt180) cc_final: 0.6651 (pmt170) REVERT: A 304 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8175 (mm-30) REVERT: A 316 LYS cc_start: 0.8667 (tttt) cc_final: 0.8211 (mtmm) REVERT: A 355 ASN cc_start: 0.6478 (m110) cc_final: 0.5938 (t0) REVERT: A 534 LYS cc_start: 0.7725 (mttt) cc_final: 0.7328 (mttt) REVERT: A 630 LYS cc_start: 0.7385 (mmtt) cc_final: 0.6836 (mtmt) REVERT: A 654 ASN cc_start: 0.7074 (m-40) cc_final: 0.6852 (m110) REVERT: A 661 GLU cc_start: 0.7923 (pt0) cc_final: 0.7003 (pp20) REVERT: B 5 LYS cc_start: 0.7338 (tttt) cc_final: 0.6946 (ttpp) REVERT: B 18 ARG cc_start: 0.7515 (mtt180) cc_final: 0.6648 (pmt170) REVERT: B 304 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8170 (mm-30) REVERT: B 316 LYS cc_start: 0.8663 (tttt) cc_final: 0.8218 (mtmm) REVERT: B 355 ASN cc_start: 0.6436 (m110) cc_final: 0.6088 (m-40) REVERT: B 534 LYS cc_start: 0.7720 (mttt) cc_final: 0.7318 (mttt) REVERT: B 630 LYS cc_start: 0.7443 (mmtt) cc_final: 0.6904 (mtmt) REVERT: B 654 ASN cc_start: 0.7062 (m-40) cc_final: 0.6840 (m110) REVERT: B 661 GLU cc_start: 0.7933 (pt0) cc_final: 0.7011 (pp20) REVERT: B 712 GLU cc_start: 0.6845 (tp30) cc_final: 0.6560 (mp0) REVERT: C 5 LYS cc_start: 0.7344 (tttt) cc_final: 0.6950 (ttpp) REVERT: C 18 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6642 (pmt170) REVERT: C 304 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8173 (mm-30) REVERT: C 316 LYS cc_start: 0.8666 (tttt) cc_final: 0.8210 (mtmm) REVERT: C 355 ASN cc_start: 0.6509 (m110) cc_final: 0.6147 (m-40) REVERT: C 372 ARG cc_start: 0.5782 (ttm-80) cc_final: 0.4956 (ttt180) REVERT: C 534 LYS cc_start: 0.7723 (mttt) cc_final: 0.7321 (mttt) REVERT: C 630 LYS cc_start: 0.7385 (mmtt) cc_final: 0.6882 (mtmt) REVERT: C 654 ASN cc_start: 0.7030 (m-40) cc_final: 0.6805 (m110) REVERT: C 661 GLU cc_start: 0.7910 (pt0) cc_final: 0.6978 (pp20) REVERT: D 5 LYS cc_start: 0.7345 (tttt) cc_final: 0.6950 (ttpp) REVERT: D 18 ARG cc_start: 0.7507 (mtt180) cc_final: 0.6640 (pmt170) REVERT: D 35 ARG cc_start: 0.5550 (mtp-110) cc_final: 0.5300 (mtp-110) REVERT: D 304 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8173 (mm-30) REVERT: D 316 LYS cc_start: 0.8665 (tttt) cc_final: 0.8218 (mtmm) REVERT: D 355 ASN cc_start: 0.6512 (m110) cc_final: 0.6148 (m-40) REVERT: D 534 LYS cc_start: 0.7726 (mttt) cc_final: 0.7325 (mttt) REVERT: D 630 LYS cc_start: 0.7378 (mmtt) cc_final: 0.6885 (mtmt) REVERT: D 654 ASN cc_start: 0.7070 (m-40) cc_final: 0.6851 (m110) REVERT: D 661 GLU cc_start: 0.7929 (pt0) cc_final: 0.7022 (pp20) REVERT: D 712 GLU cc_start: 0.6846 (tp30) cc_final: 0.6559 (mp0) outliers start: 46 outliers final: 36 residues processed: 289 average time/residue: 1.5567 time to fit residues: 516.4417 Evaluate side-chains 278 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 242 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 677 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 189 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 280 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 331 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 202 optimal weight: 0.6980 chunk 153 optimal weight: 0.0980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 707 ASN D 707 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 27768 Z= 0.115 Angle : 0.415 6.117 37764 Z= 0.220 Chirality : 0.041 0.142 4348 Planarity : 0.003 0.035 4928 Dihedral : 12.296 105.207 4308 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.84 % Allowed : 9.28 % Favored : 89.87 % 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: -0.36 (0.15), residues: 3456 helix: 0.46 (0.15), residues: 1372 sheet: 0.19 (0.20), residues: 660 loop : -1.07 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 278 HIS 0.002 0.000 HIS D 586 PHE 0.010 0.001 PHE C 638 TYR 0.016 0.001 TYR D 116 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 275 time to evaluate : 3.344 Fit side-chains REVERT: A 5 LYS cc_start: 0.7295 (tttt) cc_final: 0.6930 (ttpp) REVERT: A 18 ARG cc_start: 0.7519 (mtt180) cc_final: 0.6619 (pmt170) REVERT: A 304 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8149 (mm-30) REVERT: A 316 LYS cc_start: 0.8627 (tttt) cc_final: 0.8183 (mtmm) REVERT: A 355 ASN cc_start: 0.6296 (m110) cc_final: 0.5798 (t0) REVERT: A 372 ARG cc_start: 0.5691 (ttm-80) cc_final: 0.4886 (ttt180) REVERT: A 534 LYS cc_start: 0.7539 (mttt) cc_final: 0.7128 (mttt) REVERT: A 630 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6841 (mtmt) REVERT: A 654 ASN cc_start: 0.7109 (m-40) cc_final: 0.6901 (m110) REVERT: A 661 GLU cc_start: 0.7892 (pt0) cc_final: 0.7008 (pp20) REVERT: B 5 LYS cc_start: 0.7283 (tttt) cc_final: 0.6917 (ttpp) REVERT: B 18 ARG cc_start: 0.7515 (mtt180) cc_final: 0.6615 (pmt170) REVERT: B 304 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8141 (mm-30) REVERT: B 316 LYS cc_start: 0.8637 (tttt) cc_final: 0.8207 (mtmm) REVERT: B 355 ASN cc_start: 0.6373 (m110) cc_final: 0.5870 (t0) REVERT: B 372 ARG cc_start: 0.5686 (ttm-80) cc_final: 0.4894 (ttt180) REVERT: B 534 LYS cc_start: 0.7544 (mttt) cc_final: 0.7117 (mttt) REVERT: B 630 LYS cc_start: 0.7446 (mmtt) cc_final: 0.6916 (mtmt) REVERT: B 654 ASN cc_start: 0.7105 (m-40) cc_final: 0.6895 (m110) REVERT: B 661 GLU cc_start: 0.7890 (pt0) cc_final: 0.7010 (pp20) REVERT: B 712 GLU cc_start: 0.6783 (tp30) cc_final: 0.6524 (mp0) REVERT: C 5 LYS cc_start: 0.7291 (tttt) cc_final: 0.6922 (ttpp) REVERT: C 18 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6605 (pmt170) REVERT: C 304 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8169 (mm-30) REVERT: C 316 LYS cc_start: 0.8596 (tttt) cc_final: 0.8161 (mtmm) REVERT: C 355 ASN cc_start: 0.6398 (m110) cc_final: 0.6036 (m-40) REVERT: C 372 ARG cc_start: 0.5818 (ttm-80) cc_final: 0.5047 (ttt180) REVERT: C 534 LYS cc_start: 0.7544 (mttt) cc_final: 0.7119 (mttt) REVERT: C 630 LYS cc_start: 0.7374 (mmtt) cc_final: 0.6895 (mtmt) REVERT: C 654 ASN cc_start: 0.7117 (m-40) cc_final: 0.6892 (m110) REVERT: C 661 GLU cc_start: 0.7869 (pt0) cc_final: 0.6968 (pp20) REVERT: D 5 LYS cc_start: 0.7290 (tttt) cc_final: 0.6920 (ttpp) REVERT: D 18 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6607 (pmt170) REVERT: D 35 ARG cc_start: 0.5563 (mtp-110) cc_final: 0.5288 (mtp-110) REVERT: D 304 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8138 (mm-30) REVERT: D 316 LYS cc_start: 0.8610 (tttt) cc_final: 0.8185 (mtmm) REVERT: D 355 ASN cc_start: 0.6317 (m110) cc_final: 0.5968 (m-40) REVERT: D 372 ARG cc_start: 0.5525 (ttm-80) cc_final: 0.4751 (ttt90) REVERT: D 534 LYS cc_start: 0.7545 (mttt) cc_final: 0.7125 (mttt) REVERT: D 558 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: D 630 LYS cc_start: 0.7379 (mmtt) cc_final: 0.6909 (mtmt) REVERT: D 654 ASN cc_start: 0.7115 (m-40) cc_final: 0.6906 (m110) REVERT: D 661 GLU cc_start: 0.7883 (pt0) cc_final: 0.6994 (pp20) REVERT: D 712 GLU cc_start: 0.6787 (tp30) cc_final: 0.6525 (mp0) outliers start: 24 outliers final: 12 residues processed: 292 average time/residue: 1.5468 time to fit residues: 522.2919 Evaluate side-chains 257 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 244 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 677 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 260 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN B 191 GLN B 641 ASN D 740 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 27768 Z= 0.153 Angle : 0.432 6.067 37764 Z= 0.229 Chirality : 0.042 0.138 4348 Planarity : 0.003 0.034 4928 Dihedral : 12.145 101.662 4308 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.16 % Allowed : 9.56 % Favored : 89.28 % 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: -0.32 (0.15), residues: 3456 helix: 0.51 (0.15), residues: 1380 sheet: 0.20 (0.20), residues: 656 loop : -1.05 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 278 HIS 0.003 0.001 HIS A 586 PHE 0.009 0.001 PHE B 638 TYR 0.015 0.001 TYR B 519 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 257 time to evaluate : 3.268 Fit side-chains REVERT: A 5 LYS cc_start: 0.7299 (tttt) cc_final: 0.6934 (ttpp) REVERT: A 18 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6653 (pmt170) REVERT: A 304 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8123 (mm-30) REVERT: A 316 LYS cc_start: 0.8604 (tttt) cc_final: 0.8156 (mtmm) REVERT: A 355 ASN cc_start: 0.6335 (m110) cc_final: 0.6055 (m-40) REVERT: A 372 ARG cc_start: 0.5715 (ttm-80) cc_final: 0.4915 (ttt180) REVERT: A 534 LYS cc_start: 0.7583 (mttt) cc_final: 0.7160 (mttt) REVERT: A 558 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8235 (pt0) REVERT: A 630 LYS cc_start: 0.7387 (mmtt) cc_final: 0.6848 (mtmt) REVERT: A 654 ASN cc_start: 0.7081 (m-40) cc_final: 0.6859 (m110) REVERT: A 661 GLU cc_start: 0.7893 (pt0) cc_final: 0.6987 (pp20) REVERT: B 5 LYS cc_start: 0.7288 (tttt) cc_final: 0.6923 (ttpp) REVERT: B 18 ARG cc_start: 0.7516 (mtt180) cc_final: 0.6616 (pmt170) REVERT: B 304 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8139 (mm-30) REVERT: B 316 LYS cc_start: 0.8614 (tttt) cc_final: 0.8185 (mtmm) REVERT: B 355 ASN cc_start: 0.6370 (m110) cc_final: 0.6091 (m-40) REVERT: B 372 ARG cc_start: 0.5702 (ttm-80) cc_final: 0.4843 (ttt90) REVERT: B 534 LYS cc_start: 0.7553 (mttt) cc_final: 0.7118 (mttt) REVERT: B 558 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8202 (pt0) REVERT: B 654 ASN cc_start: 0.7076 (m-40) cc_final: 0.6847 (m110) REVERT: B 661 GLU cc_start: 0.7897 (pt0) cc_final: 0.6994 (pp20) REVERT: B 712 GLU cc_start: 0.6819 (tp30) cc_final: 0.6542 (mp0) REVERT: C 5 LYS cc_start: 0.7295 (tttt) cc_final: 0.6927 (ttpp) REVERT: C 18 ARG cc_start: 0.7510 (mtt180) cc_final: 0.6612 (pmt170) REVERT: C 304 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8141 (mm-30) REVERT: C 316 LYS cc_start: 0.8615 (tttt) cc_final: 0.8174 (mtmm) REVERT: C 355 ASN cc_start: 0.6342 (m110) cc_final: 0.5827 (t0) REVERT: C 372 ARG cc_start: 0.5764 (ttm-80) cc_final: 0.4977 (ttt90) REVERT: C 534 LYS cc_start: 0.7566 (mttt) cc_final: 0.7129 (mttt) REVERT: C 558 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: C 630 LYS cc_start: 0.7378 (mmtt) cc_final: 0.6896 (mtmt) REVERT: C 654 ASN cc_start: 0.7105 (m-40) cc_final: 0.6884 (m110) REVERT: C 661 GLU cc_start: 0.7896 (pt0) cc_final: 0.6988 (pp20) REVERT: D 5 LYS cc_start: 0.7295 (tttt) cc_final: 0.6924 (ttpp) REVERT: D 18 ARG cc_start: 0.7509 (mtt180) cc_final: 0.6610 (pmt170) REVERT: D 35 ARG cc_start: 0.5783 (mtp-110) cc_final: 0.5499 (mtp-110) REVERT: D 304 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8139 (mm-30) REVERT: D 316 LYS cc_start: 0.8614 (tttt) cc_final: 0.8186 (mtmm) REVERT: D 346 ASP cc_start: 0.5067 (t0) cc_final: 0.4865 (t0) REVERT: D 355 ASN cc_start: 0.6315 (m110) cc_final: 0.5970 (m-40) REVERT: D 372 ARG cc_start: 0.5559 (ttm-80) cc_final: 0.4770 (ttt90) REVERT: D 534 LYS cc_start: 0.7554 (mttt) cc_final: 0.7121 (mttt) REVERT: D 558 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8217 (pt0) REVERT: D 630 LYS cc_start: 0.7380 (mmtt) cc_final: 0.6911 (mtmt) REVERT: D 654 ASN cc_start: 0.7084 (m-40) cc_final: 0.6860 (m110) REVERT: D 661 GLU cc_start: 0.7924 (pt0) cc_final: 0.7000 (pp20) REVERT: D 712 GLU cc_start: 0.6825 (tp30) cc_final: 0.6546 (mp0) outliers start: 33 outliers final: 22 residues processed: 280 average time/residue: 1.6596 time to fit residues: 538.1183 Evaluate side-chains 278 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 677 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 289 optimal weight: 0.0980 chunk 308 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 242 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 307 optimal weight: 0.0770 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 707 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 27768 Z= 0.194 Angle : 0.470 5.756 37764 Z= 0.250 Chirality : 0.043 0.145 4348 Planarity : 0.003 0.035 4928 Dihedral : 12.113 95.363 4308 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.13 % Allowed : 9.56 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3456 helix: 0.40 (0.15), residues: 1384 sheet: 0.05 (0.20), residues: 668 loop : -1.12 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 278 HIS 0.004 0.001 HIS B 586 PHE 0.010 0.001 PHE D 638 TYR 0.013 0.001 TYR C 116 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 3.061 Fit side-chains REVERT: A 5 LYS cc_start: 0.7306 (tttt) cc_final: 0.6975 (ttpp) REVERT: A 18 ARG cc_start: 0.7529 (mtt180) cc_final: 0.6653 (pmt170) REVERT: A 304 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8130 (mm-30) REVERT: A 316 LYS cc_start: 0.8665 (tttt) cc_final: 0.8209 (mtmm) REVERT: A 355 ASN cc_start: 0.6404 (m110) cc_final: 0.6109 (m-40) REVERT: A 372 ARG cc_start: 0.5776 (ttm-80) cc_final: 0.4967 (ttt180) REVERT: A 534 LYS cc_start: 0.7732 (mttt) cc_final: 0.7287 (mttt) REVERT: A 558 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: A 654 ASN cc_start: 0.7036 (m-40) cc_final: 0.6814 (m110) REVERT: A 661 GLU cc_start: 0.7944 (pt0) cc_final: 0.7026 (pp20) REVERT: B 5 LYS cc_start: 0.7297 (tttt) cc_final: 0.6967 (ttpp) REVERT: B 18 ARG cc_start: 0.7527 (mtt180) cc_final: 0.6650 (pmt170) REVERT: B 304 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8122 (mm-30) REVERT: B 316 LYS cc_start: 0.8657 (tttt) cc_final: 0.8215 (mtmm) REVERT: B 355 ASN cc_start: 0.6460 (m110) cc_final: 0.6169 (m-40) REVERT: B 372 ARG cc_start: 0.5770 (ttm-80) cc_final: 0.4963 (ttt180) REVERT: B 534 LYS cc_start: 0.7656 (mttt) cc_final: 0.7218 (mttt) REVERT: B 558 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: B 654 ASN cc_start: 0.7079 (m-40) cc_final: 0.6841 (m110) REVERT: B 661 GLU cc_start: 0.7933 (pt0) cc_final: 0.7004 (pp20) REVERT: B 712 GLU cc_start: 0.6866 (tp30) cc_final: 0.6576 (mp0) REVERT: C 5 LYS cc_start: 0.7302 (tttt) cc_final: 0.6968 (ttpp) REVERT: C 18 ARG cc_start: 0.7518 (mtt180) cc_final: 0.6646 (pmt170) REVERT: C 182 MET cc_start: 0.8492 (mtp) cc_final: 0.8118 (mtm) REVERT: C 304 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8127 (mm-30) REVERT: C 316 LYS cc_start: 0.8662 (tttt) cc_final: 0.8205 (mtmm) REVERT: C 355 ASN cc_start: 0.6381 (m110) cc_final: 0.5868 (t0) REVERT: C 372 ARG cc_start: 0.5773 (ttm-80) cc_final: 0.4974 (ttt180) REVERT: C 534 LYS cc_start: 0.7729 (mttt) cc_final: 0.7278 (mttt) REVERT: C 558 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: C 654 ASN cc_start: 0.7045 (m-40) cc_final: 0.6808 (m110) REVERT: C 661 GLU cc_start: 0.7948 (pt0) cc_final: 0.7025 (pp20) REVERT: D 5 LYS cc_start: 0.7301 (tttt) cc_final: 0.6966 (ttpp) REVERT: D 18 ARG cc_start: 0.7516 (mtt180) cc_final: 0.6644 (pmt170) REVERT: D 35 ARG cc_start: 0.5650 (mtp-110) cc_final: 0.5370 (mtp-110) REVERT: D 182 MET cc_start: 0.8497 (mtp) cc_final: 0.8115 (mtm) REVERT: D 304 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8117 (mm-30) REVERT: D 316 LYS cc_start: 0.8661 (tttt) cc_final: 0.8214 (mtmm) REVERT: D 355 ASN cc_start: 0.6379 (m110) cc_final: 0.5883 (t0) REVERT: D 372 ARG cc_start: 0.5615 (ttm-80) cc_final: 0.4808 (ttt90) REVERT: D 534 LYS cc_start: 0.7654 (mttt) cc_final: 0.7219 (mttt) REVERT: D 558 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: D 654 ASN cc_start: 0.7078 (m-40) cc_final: 0.6843 (m110) REVERT: D 661 GLU cc_start: 0.7936 (pt0) cc_final: 0.7000 (pp20) REVERT: D 712 GLU cc_start: 0.6870 (tp30) cc_final: 0.6582 (mp0) outliers start: 32 outliers final: 24 residues processed: 272 average time/residue: 1.6202 time to fit residues: 503.5178 Evaluate side-chains 274 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 246 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 677 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 154 optimal weight: 0.2980 chunk 227 optimal weight: 4.9990 chunk 342 optimal weight: 20.0000 chunk 315 optimal weight: 1.9990 chunk 272 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 740 HIS C 707 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 27768 Z= 0.219 Angle : 0.473 4.996 37764 Z= 0.252 Chirality : 0.043 0.141 4348 Planarity : 0.003 0.036 4928 Dihedral : 12.072 96.370 4308 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.20 % Allowed : 9.56 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3456 helix: 0.36 (0.15), residues: 1384 sheet: 0.14 (0.20), residues: 656 loop : -1.14 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 181 HIS 0.004 0.001 HIS B 586 PHE 0.010 0.001 PHE B 638 TYR 0.015 0.001 TYR C 519 ARG 0.003 0.000 ARG C 511 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 247 time to evaluate : 3.253 Fit side-chains REVERT: A 5 LYS cc_start: 0.7295 (tttt) cc_final: 0.6978 (ttpp) REVERT: A 18 ARG cc_start: 0.7538 (mtt180) cc_final: 0.6660 (pmt170) REVERT: A 304 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8127 (mm-30) REVERT: A 316 LYS cc_start: 0.8683 (tttt) cc_final: 0.8189 (mtmm) REVERT: A 355 ASN cc_start: 0.6450 (m110) cc_final: 0.6166 (m-40) REVERT: A 372 ARG cc_start: 0.5804 (ttm-80) cc_final: 0.4986 (ttt180) REVERT: A 534 LYS cc_start: 0.7741 (mttt) cc_final: 0.7301 (mttt) REVERT: A 558 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: A 654 ASN cc_start: 0.7045 (m-40) cc_final: 0.6821 (m110) REVERT: A 661 GLU cc_start: 0.7947 (pt0) cc_final: 0.7023 (pp20) REVERT: B 5 LYS cc_start: 0.7309 (tttt) cc_final: 0.6981 (ttpp) REVERT: B 18 ARG cc_start: 0.7536 (mtt180) cc_final: 0.6658 (pmt170) REVERT: B 304 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8129 (mm-30) REVERT: B 316 LYS cc_start: 0.8700 (tttt) cc_final: 0.8208 (mtmm) REVERT: B 355 ASN cc_start: 0.6463 (m110) cc_final: 0.6170 (m-40) REVERT: B 372 ARG cc_start: 0.5794 (ttm-80) cc_final: 0.4968 (ttt180) REVERT: B 534 LYS cc_start: 0.7730 (mttt) cc_final: 0.7295 (mttt) REVERT: B 558 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: B 654 ASN cc_start: 0.7052 (m-40) cc_final: 0.6818 (m110) REVERT: B 661 GLU cc_start: 0.7954 (pt0) cc_final: 0.7029 (pp20) REVERT: B 712 GLU cc_start: 0.6875 (tp30) cc_final: 0.6586 (mp0) REVERT: C 5 LYS cc_start: 0.7315 (tttt) cc_final: 0.6983 (ttpp) REVERT: C 18 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6647 (pmt170) REVERT: C 182 MET cc_start: 0.8498 (mtp) cc_final: 0.8131 (mtm) REVERT: C 304 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8132 (mm-30) REVERT: C 316 LYS cc_start: 0.8699 (tttt) cc_final: 0.8208 (mtmm) REVERT: C 355 ASN cc_start: 0.6415 (m110) cc_final: 0.6120 (m-40) REVERT: C 372 ARG cc_start: 0.5828 (ttm-80) cc_final: 0.5060 (ttt180) REVERT: C 534 LYS cc_start: 0.7748 (mttt) cc_final: 0.7305 (mttt) REVERT: C 558 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8308 (pt0) REVERT: C 654 ASN cc_start: 0.7043 (m-40) cc_final: 0.6814 (m110) REVERT: C 661 GLU cc_start: 0.7953 (pt0) cc_final: 0.7025 (pp20) REVERT: D 5 LYS cc_start: 0.7298 (tttt) cc_final: 0.6964 (ttpp) REVERT: D 18 ARG cc_start: 0.7532 (mtt180) cc_final: 0.6647 (pmt170) REVERT: D 35 ARG cc_start: 0.5610 (mtp-110) cc_final: 0.5349 (mtp-110) REVERT: D 182 MET cc_start: 0.8494 (mtp) cc_final: 0.8118 (mtm) REVERT: D 304 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8124 (mm-30) REVERT: D 316 LYS cc_start: 0.8698 (tttt) cc_final: 0.8215 (mtmm) REVERT: D 355 ASN cc_start: 0.6446 (m110) cc_final: 0.5926 (t0) REVERT: D 372 ARG cc_start: 0.5726 (ttm-80) cc_final: 0.4927 (ttt180) REVERT: D 534 LYS cc_start: 0.7736 (mttt) cc_final: 0.7294 (mttt) REVERT: D 558 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: D 654 ASN cc_start: 0.7052 (m-40) cc_final: 0.6821 (m110) REVERT: D 661 GLU cc_start: 0.7955 (pt0) cc_final: 0.7028 (pp20) outliers start: 34 outliers final: 28 residues processed: 273 average time/residue: 1.5487 time to fit residues: 487.2411 Evaluate side-chains 278 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 677 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 2.9990 chunk 290 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 251 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 273 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 280 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 ASN B 707 ASN C 707 ASN D 707 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.190644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114336 restraints weight = 29511.575| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.75 r_work: 0.3070 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 27768 Z= 0.264 Angle : 0.512 5.510 37764 Z= 0.273 Chirality : 0.044 0.149 4348 Planarity : 0.004 0.038 4928 Dihedral : 12.259 99.409 4308 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.30 % Allowed : 9.60 % Favored : 89.10 % 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: -0.61 (0.14), residues: 3456 helix: 0.28 (0.15), residues: 1356 sheet: -0.06 (0.20), residues: 692 loop : -1.17 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 181 HIS 0.005 0.001 HIS D 586 PHE 0.012 0.001 PHE A 58 TYR 0.014 0.002 TYR C 519 ARG 0.003 0.000 ARG C 511 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9973.83 seconds wall clock time: 177 minutes 39.18 seconds (10659.18 seconds total)