Starting phenix.real_space_refine on Tue Feb 20 05:47:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg5_23311/02_2024/7lg5_23311_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg5_23311/02_2024/7lg5_23311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg5_23311/02_2024/7lg5_23311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg5_23311/02_2024/7lg5_23311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg5_23311/02_2024/7lg5_23311_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lg5_23311/02_2024/7lg5_23311_neut_updated.pdb" } resolution = 2.63 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= 0.004 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 12 5.21 5 S 96 5.16 5 C 16828 2.51 5 N 4696 2.21 5 O 5232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "D GLU 558": "OE1" <-> "OE2" Residue "D GLU 677": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6657 Classifications: {'peptide': 871} Link IDs: {'PTRANS': 40, 'TRANS': 830} Chain breaks: 1 Chain: "B" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6657 Classifications: {'peptide': 871} Link IDs: {'PTRANS': 40, 'TRANS': 830} Chain breaks: 1 Chain: "C" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6657 Classifications: {'peptide': 871} Link IDs: {'PTRANS': 40, 'TRANS': 830} Chain breaks: 1 Chain: "D" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6657 Classifications: {'peptide': 871} Link IDs: {'PTRANS': 40, 'TRANS': 830} Chain breaks: 1 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 14.22, per 1000 atoms: 0.53 Number of scatterers: 26888 At special positions: 0 Unit cell: (135.945, 147.915, 144.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 24 15.00 Mg 12 11.99 O 5232 8.00 N 4696 7.00 C 16828 6.00 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: 10.46 Conformation dependent library (CDL) restraints added in 5.5 seconds 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 24 sheets defined 34.1% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.07 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.906A pdb=" N VAL A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 137 removed outlier: 3.588A pdb=" N VAL A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 3.796A pdb=" N GLU A 148 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS A 149 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 158 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.524A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) 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: 3.607A pdb=" N ALA A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 5.188A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 removed outlier: 4.097A 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: 3.734A 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: 3.716A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.627A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.881A 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: 3.575A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 removed outlier: 3.865A pdb=" N ALA A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 4.921A 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: 3.685A 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 720 Processing helix chain 'A' and resid 750 through 761 removed outlier: 3.702A pdb=" N ALA A 755 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 756 " --> pdb=" O TYR A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 859 through 869 removed outlier: 3.881A pdb=" N ILE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.906A pdb=" N VAL B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 137 removed outlier: 3.588A pdb=" N VAL B 137 " --> pdb=" O CYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 removed outlier: 3.796A pdb=" N GLU B 148 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS B 149 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 158 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.525A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) 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: 3.607A pdb=" N ALA B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 5.188A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 removed outlier: 4.097A 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: 3.734A 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: 3.716A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 513 removed outlier: 3.627A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.882A 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: 3.576A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 629 removed outlier: 3.865A 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: 4.243A pdb=" N ALA B 628 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 4.922A 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: 3.685A 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 720 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.701A pdb=" N ALA B 755 " --> pdb=" O GLY B 752 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 756 " --> pdb=" O TYR B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 789 Processing helix chain 'B' and resid 811 through 824 Processing helix chain 'B' and resid 859 through 869 removed outlier: 3.880A pdb=" N ILE B 866 " --> pdb=" O ALA B 862 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.905A pdb=" N VAL C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 137 removed outlier: 3.588A pdb=" N VAL C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 3.796A pdb=" N GLU C 148 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS C 149 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 158 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.525A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) 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: 3.608A pdb=" N ALA C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 253 removed outlier: 5.188A pdb=" N ASN C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 4.098A 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: 3.734A 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: 3.715A pdb=" N MET C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 513 removed outlier: 3.627A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.881A 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: 3.576A pdb=" N LYS C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 629 removed outlier: 3.864A pdb=" N ALA C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA C 628 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP C 629 " --> pdb=" O ALA C 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 622 through 629' Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.685A 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: 3.701A pdb=" N ALA C 755 " --> pdb=" O GLY C 752 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 756 " --> pdb=" O TYR C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 789 Processing helix chain 'C' and resid 811 through 824 Processing helix chain 'C' and resid 859 through 869 removed outlier: 3.881A pdb=" N ILE C 866 " --> pdb=" O ALA C 862 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG C 869 " --> pdb=" O LEU C 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 80 through 92 removed outlier: 3.906A pdb=" N VAL D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 137 removed outlier: 3.588A pdb=" N VAL D 137 " --> pdb=" O CYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 removed outlier: 3.797A pdb=" N GLU D 148 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 158 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 removed outlier: 3.524A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) 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: 3.607A pdb=" N ALA D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 253 removed outlier: 5.188A pdb=" N ASN D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 290 removed outlier: 4.097A 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: 3.734A 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: 3.716A pdb=" N MET D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 513 removed outlier: 3.626A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 removed outlier: 3.881A 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: 3.575A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 629 removed outlier: 3.865A pdb=" N ALA D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA D 628 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASP D 629 " --> pdb=" O ALA D 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 622 through 629' Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.686A 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 720 Processing helix chain 'D' and resid 750 through 761 removed outlier: 3.702A pdb=" N ALA D 755 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 756 " --> pdb=" O TYR D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 789 Processing helix chain 'D' and resid 811 through 824 Processing helix chain 'D' and resid 859 through 869 removed outlier: 3.881A pdb=" N ILE D 866 " --> pdb=" O ALA D 862 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 99 through 104 removed outlier: 4.292A pdb=" N VAL A 109 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 5.782A 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: 6.743A pdb=" N LEU A 311 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 320 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU A 322 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP A 307 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.659A 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: 6.820A pdb=" N LEU A 665 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 635 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.100A 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: 7.754A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 527 " --> pdb=" O CYS A 531 " (cutoff:3.500A) removed outlier: 5.472A 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: 4.291A pdb=" N VAL B 109 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 5.783A 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: 6.744A pdb=" N LEU B 311 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL B 320 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU B 322 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP B 307 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.660A 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: 6.820A pdb=" N LEU B 665 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL B 635 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.790A 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: 7.755A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 527 " --> pdb=" O CYS B 531 " (cutoff:3.500A) removed outlier: 5.472A 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: 4.291A pdb=" N VAL C 109 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 5.781A 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: 6.744A pdb=" N LEU C 311 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL C 320 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG C 309 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU C 322 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP C 307 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.659A 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: 6.820A pdb=" N LEU C 665 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL C 635 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 527 " --> pdb=" O CYS C 531 " (cutoff:3.500A) removed outlier: 5.471A 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: 4.292A pdb=" N VAL D 109 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 5.783A 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: 6.743A pdb=" N LEU D 311 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL D 320 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG D 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU D 322 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP D 307 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.659A 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: 6.820A pdb=" N LEU D 665 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL D 635 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 9.100A 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: 7.754A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 527 " --> pdb=" O CYS D 531 " (cutoff:3.500A) removed outlier: 5.472A 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 736 940 hydrogen bonds defined for protein. 2508 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: 11.62 Time building geometry restraints manager: 11.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4677 1.29 - 1.43: 6547 1.43 - 1.57: 15732 1.57 - 1.70: 220 1.70 - 1.84: 168 Bond restraints: 27344 Sorted by residual: bond pdb=" C PRO C 481 " pdb=" O PRO C 481 " ideal model delta sigma weight residual 1.240 1.156 0.084 1.12e-02 7.97e+03 5.66e+01 bond pdb=" C PRO B 481 " pdb=" O PRO B 481 " ideal model delta sigma weight residual 1.240 1.156 0.084 1.12e-02 7.97e+03 5.63e+01 bond pdb=" C PRO A 481 " pdb=" O PRO A 481 " ideal model delta sigma weight residual 1.240 1.156 0.084 1.12e-02 7.97e+03 5.63e+01 bond pdb=" C PRO D 481 " pdb=" O PRO D 481 " ideal model delta sigma weight residual 1.240 1.157 0.084 1.12e-02 7.97e+03 5.59e+01 bond pdb=" NE ARG A 35 " pdb=" CZ ARG A 35 " ideal model delta sigma weight residual 1.326 1.384 -0.058 1.10e-02 8.26e+03 2.82e+01 ... (remaining 27339 not shown) Histogram of bond angle deviations from ideal: 95.42 - 104.40: 553 104.40 - 113.38: 14365 113.38 - 122.36: 17833 122.36 - 131.34: 4393 131.34 - 140.32: 68 Bond angle restraints: 37212 Sorted by residual: angle pdb=" N LEU A 843 " pdb=" CA LEU A 843 " pdb=" C LEU A 843 " ideal model delta sigma weight residual 113.50 97.40 16.10 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N LEU B 843 " pdb=" CA LEU B 843 " pdb=" C LEU B 843 " ideal model delta sigma weight residual 113.50 97.40 16.10 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N LEU C 843 " pdb=" CA LEU C 843 " pdb=" C LEU C 843 " ideal model delta sigma weight residual 113.50 97.41 16.09 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N LEU D 843 " pdb=" CA LEU D 843 " pdb=" C LEU D 843 " ideal model delta sigma weight residual 113.50 97.43 16.07 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N GLY D 78 " pdb=" CA GLY D 78 " pdb=" C GLY D 78 " ideal model delta sigma weight residual 112.82 97.67 15.15 1.38e+00 5.25e-01 1.21e+02 ... (remaining 37207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15943 17.99 - 35.98: 437 35.98 - 53.97: 156 53.97 - 71.95: 60 71.95 - 89.94: 28 Dihedral angle restraints: 16624 sinusoidal: 6712 harmonic: 9912 Sorted by residual: dihedral pdb=" C LEU C 425 " pdb=" N LEU C 425 " pdb=" CA LEU C 425 " pdb=" CB LEU C 425 " ideal model delta harmonic sigma weight residual -122.60 -112.27 -10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" C LEU D 425 " pdb=" N LEU D 425 " pdb=" CA LEU D 425 " pdb=" CB LEU D 425 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" C LEU A 425 " pdb=" N LEU A 425 " pdb=" CA LEU A 425 " pdb=" CB LEU A 425 " ideal model delta harmonic sigma weight residual -122.60 -112.31 -10.29 0 2.50e+00 1.60e-01 1.69e+01 ... (remaining 16621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2994 0.092 - 0.183: 1013 0.183 - 0.275: 249 0.275 - 0.366: 32 0.366 - 0.457: 12 Chirality restraints: 4300 Sorted by residual: chirality pdb=" CA PRO B 481 " pdb=" N PRO B 481 " pdb=" C PRO B 481 " pdb=" CB PRO B 481 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA PRO C 481 " pdb=" N PRO C 481 " pdb=" C PRO C 481 " pdb=" CB PRO C 481 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA PRO A 481 " pdb=" N PRO A 481 " pdb=" C PRO A 481 " pdb=" CB PRO A 481 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 4297 not shown) Planarity restraints: 4840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 780 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C SER D 780 " -0.067 2.00e-02 2.50e+03 pdb=" O SER D 780 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP D 781 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 780 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C SER A 780 " -0.067 2.00e-02 2.50e+03 pdb=" O SER A 780 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A 781 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 780 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C SER B 780 " 0.067 2.00e-02 2.50e+03 pdb=" O SER B 780 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B 781 " -0.022 2.00e-02 2.50e+03 ... (remaining 4837 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 28 2.39 - 3.02: 15331 3.02 - 3.65: 37611 3.65 - 4.27: 62491 4.27 - 4.90: 100074 Nonbonded interactions: 215535 Sorted by model distance: nonbonded pdb=" OE2 GLU B 558 " pdb="MG MG B 903 " model vdw 1.766 2.170 nonbonded pdb=" OE2 GLU A 558 " pdb="MG MG A 903 " model vdw 1.766 2.170 nonbonded pdb=" OE2 GLU C 558 " pdb="MG MG C 903 " model vdw 1.766 2.170 nonbonded pdb=" OE2 GLU D 558 " pdb="MG MG D 903 " model vdw 1.766 2.170 nonbonded pdb=" OG1 THR D 500 " pdb="MG MG D 903 " model vdw 1.982 2.170 ... (remaining 215530 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.450 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 73.570 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.170 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.018 0.131 27344 Z= 1.233 Angle : 1.830 16.100 37212 Z= 1.245 Chirality : 0.098 0.457 4300 Planarity : 0.009 0.071 4840 Dihedral : 11.601 89.942 10304 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.13 % 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: -0.64 (0.13), residues: 3468 helix: -1.08 (0.13), residues: 1272 sheet: 1.47 (0.21), residues: 548 loop : -0.42 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.005 TRP A 763 HIS 0.019 0.003 HIS B 586 PHE 0.034 0.006 PHE C 768 TYR 0.038 0.007 TYR C 285 ARG 0.009 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 CYS cc_start: 0.8489 (m) cc_final: 0.8175 (p) REVERT: A 243 PHE cc_start: 0.6625 (m-10) cc_final: 0.6393 (m-80) REVERT: B 133 CYS cc_start: 0.8491 (m) cc_final: 0.8170 (p) REVERT: B 243 PHE cc_start: 0.6484 (m-10) cc_final: 0.6246 (m-80) REVERT: C 133 CYS cc_start: 0.8534 (m) cc_final: 0.8211 (p) REVERT: C 243 PHE cc_start: 0.6699 (m-10) cc_final: 0.6482 (m-80) REVERT: D 133 CYS cc_start: 0.8467 (m) cc_final: 0.8154 (p) REVERT: D 243 PHE cc_start: 0.6685 (m-10) cc_final: 0.6458 (m-80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 1.3861 time to fit residues: 341.2080 Evaluate side-chains 107 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 316 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 HIS A 840 ASN B 353 HIS B 740 HIS B 840 ASN C 740 HIS D 740 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27344 Z= 0.196 Angle : 0.624 8.476 37212 Z= 0.341 Chirality : 0.046 0.167 4300 Planarity : 0.005 0.041 4840 Dihedral : 9.498 89.696 4072 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.88 % Allowed : 4.32 % Favored : 94.80 % 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: -0.23 (0.14), residues: 3468 helix: -0.05 (0.14), residues: 1308 sheet: 1.25 (0.24), residues: 508 loop : -0.60 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 278 HIS 0.010 0.001 HIS B 83 PHE 0.011 0.001 PHE D 855 TYR 0.013 0.002 TYR D 14 ARG 0.006 0.001 ARG C 754 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 ILE cc_start: 0.8187 (mt) cc_final: 0.7914 (mm) REVERT: B 820 ILE cc_start: 0.8103 (mt) cc_final: 0.7840 (mm) REVERT: C 353 HIS cc_start: 0.8929 (m90) cc_final: 0.8718 (m170) REVERT: D 353 HIS cc_start: 0.8913 (m90) cc_final: 0.8692 (m170) outliers start: 25 outliers final: 15 residues processed: 138 average time/residue: 1.2524 time to fit residues: 207.3316 Evaluate side-chains 118 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 316 optimal weight: 6.9990 chunk 342 optimal weight: 0.9980 chunk 281 optimal weight: 0.7980 chunk 313 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 ASN A 748 HIS A 840 ASN B 353 HIS B 707 ASN B 748 HIS C 748 HIS C 840 ASN D 707 ASN D 748 HIS D 840 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 27344 Z= 0.304 Angle : 0.621 16.228 37212 Z= 0.331 Chirality : 0.046 0.256 4300 Planarity : 0.005 0.076 4840 Dihedral : 9.209 88.561 4072 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.54 % Allowed : 5.93 % Favored : 92.52 % 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: -0.05 (0.14), residues: 3468 helix: 0.37 (0.15), residues: 1256 sheet: 0.90 (0.21), residues: 592 loop : -0.65 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 278 HIS 0.004 0.001 HIS C 650 PHE 0.015 0.002 PHE D 457 TYR 0.013 0.002 TYR B 530 ARG 0.007 0.001 ARG A 805 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 118 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 VAL cc_start: 0.7085 (OUTLIER) cc_final: 0.6850 (m) REVERT: B 739 GLN cc_start: 0.9022 (pp30) cc_final: 0.8819 (pp30) REVERT: B 798 VAL cc_start: 0.7122 (OUTLIER) cc_final: 0.6893 (m) REVERT: D 739 GLN cc_start: 0.9020 (pp30) cc_final: 0.8808 (pp30) outliers start: 44 outliers final: 16 residues processed: 151 average time/residue: 1.3193 time to fit residues: 236.3145 Evaluate side-chains 117 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 740 HIS Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 740 HIS Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.6980 chunk 238 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 317 optimal weight: 1.9990 chunk 336 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN A 707 ASN A 716 GLN A 840 ASN B 353 HIS B 512 GLN B 707 ASN B 716 GLN C 512 GLN C 716 GLN D 512 GLN D 716 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27344 Z= 0.273 Angle : 0.552 10.646 37212 Z= 0.292 Chirality : 0.045 0.217 4300 Planarity : 0.004 0.036 4840 Dihedral : 8.823 86.213 4072 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.93 % Allowed : 5.97 % Favored : 92.10 % 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: -0.16 (0.14), residues: 3468 helix: 0.35 (0.15), residues: 1272 sheet: 0.96 (0.21), residues: 556 loop : -0.80 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 278 HIS 0.003 0.001 HIS C 83 PHE 0.009 0.001 PHE B 638 TYR 0.011 0.001 TYR B 519 ARG 0.006 0.000 ARG B 805 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 103 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLN cc_start: 0.9030 (pp30) cc_final: 0.8808 (pp30) REVERT: D 739 GLN cc_start: 0.9018 (pp30) cc_final: 0.8770 (pp30) outliers start: 55 outliers final: 32 residues processed: 144 average time/residue: 1.2685 time to fit residues: 217.4142 Evaluate side-chains 134 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 HIS Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 866 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 250 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 287 optimal weight: 20.0000 chunk 232 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 171 optimal weight: 20.0000 chunk 301 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN B 353 HIS B 741 HIS C 840 ASN D 741 HIS D 840 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27344 Z= 0.270 Angle : 0.537 10.201 37212 Z= 0.284 Chirality : 0.044 0.203 4300 Planarity : 0.004 0.038 4840 Dihedral : 8.612 85.544 4072 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.62 % Allowed : 6.07 % Favored : 92.31 % 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: -0.15 (0.14), residues: 3468 helix: 0.45 (0.15), residues: 1272 sheet: 0.77 (0.21), residues: 624 loop : -0.86 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 278 HIS 0.003 0.001 HIS C 650 PHE 0.009 0.001 PHE D 638 TYR 0.012 0.001 TYR B 519 ARG 0.005 0.000 ARG B 805 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8791 (pp30) REVERT: D 739 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8763 (pp30) outliers start: 46 outliers final: 18 residues processed: 145 average time/residue: 1.2467 time to fit residues: 217.0161 Evaluate side-chains 123 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 20.0000 chunk 302 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 ASN A 741 HIS A 840 ASN B 353 HIS C 741 HIS C 840 ASN D 840 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27344 Z= 0.224 Angle : 0.518 10.911 37212 Z= 0.270 Chirality : 0.044 0.220 4300 Planarity : 0.004 0.038 4840 Dihedral : 8.405 85.099 4072 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.23 % Allowed : 6.71 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3468 helix: 0.60 (0.15), residues: 1272 sheet: 0.73 (0.21), residues: 584 loop : -0.85 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 278 HIS 0.003 0.001 HIS C 277 PHE 0.008 0.001 PHE B 638 TYR 0.011 0.001 TYR B 519 ARG 0.004 0.000 ARG B 805 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 103 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8745 (pp30) REVERT: D 739 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8712 (pp30) outliers start: 35 outliers final: 19 residues processed: 131 average time/residue: 1.2421 time to fit residues: 195.6524 Evaluate side-chains 122 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 3.151 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 768 PHE 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 246 LEU Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 283 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 335 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 ASN A 840 ASN B 353 HIS B 840 ASN C 707 ASN C 840 ASN D 840 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 27344 Z= 0.254 Angle : 0.529 11.487 37212 Z= 0.276 Chirality : 0.044 0.190 4300 Planarity : 0.004 0.039 4840 Dihedral : 8.345 86.107 4072 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.91 % Allowed : 7.72 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3468 helix: 0.47 (0.15), residues: 1320 sheet: 0.72 (0.21), residues: 584 loop : -0.89 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 278 HIS 0.004 0.001 HIS B 277 PHE 0.009 0.001 PHE C 638 TYR 0.013 0.001 TYR D 519 ARG 0.007 0.000 ARG D 861 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8677 (pp30) REVERT: D 739 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8663 (pp30) outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 1.3802 time to fit residues: 201.3332 Evaluate side-chains 118 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 3.016 ------------------------------------------------------------------------------- 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 768 PHE 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 246 LEU Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 200 optimal weight: 0.0770 chunk 101 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN B 353 HIS B 840 ASN C 707 ASN C 840 ASN D 840 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27344 Z= 0.218 Angle : 0.508 12.172 37212 Z= 0.263 Chirality : 0.044 0.193 4300 Planarity : 0.003 0.039 4840 Dihedral : 8.208 85.701 4072 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.84 % Allowed : 7.87 % Favored : 91.29 % 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: -0.10 (0.15), residues: 3468 helix: 0.58 (0.15), residues: 1320 sheet: 0.73 (0.21), residues: 588 loop : -0.90 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 278 HIS 0.002 0.001 HIS C 83 PHE 0.008 0.001 PHE A 638 TYR 0.011 0.001 TYR C 519 ARG 0.002 0.000 ARG C 795 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8666 (pp30) REVERT: D 739 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8658 (pp30) outliers start: 24 outliers final: 18 residues processed: 122 average time/residue: 1.2559 time to fit residues: 183.5529 Evaluate side-chains 119 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 3.574 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 768 PHE 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 246 LEU Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.7980 chunk 321 optimal weight: 0.4980 chunk 293 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 245 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 295 optimal weight: 8.9990 chunk 311 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN B 353 HIS ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 ASN ** C 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 ASN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27344 Z= 0.126 Angle : 0.490 12.959 37212 Z= 0.252 Chirality : 0.043 0.185 4300 Planarity : 0.003 0.038 4840 Dihedral : 7.751 82.853 4072 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.81 % Allowed : 7.90 % Favored : 91.29 % 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: 0.05 (0.15), residues: 3468 helix: 0.71 (0.15), residues: 1320 sheet: 0.87 (0.22), residues: 588 loop : -0.86 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 278 HIS 0.003 0.000 HIS D 83 PHE 0.008 0.001 PHE B 692 TYR 0.010 0.001 TYR A 519 ARG 0.003 0.000 ARG D 861 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8698 (pp30) REVERT: D 739 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8656 (pp30) outliers start: 23 outliers final: 16 residues processed: 119 average time/residue: 1.3018 time to fit residues: 186.8077 Evaluate side-chains 117 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 201 optimal weight: 0.0170 chunk 156 optimal weight: 0.6980 chunk 229 optimal weight: 7.9990 chunk 346 optimal weight: 30.0000 chunk 319 optimal weight: 0.9990 chunk 276 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 169 optimal weight: 30.0000 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 ASN ** C 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 ASN C 840 ASN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27344 Z= 0.143 Angle : 0.501 13.856 37212 Z= 0.255 Chirality : 0.043 0.183 4300 Planarity : 0.003 0.037 4840 Dihedral : 7.555 82.508 4072 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.67 % Allowed : 8.39 % Favored : 90.94 % 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: 0.10 (0.15), residues: 3468 helix: 0.75 (0.15), residues: 1324 sheet: 0.98 (0.21), residues: 584 loop : -0.85 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 278 HIS 0.002 0.000 HIS C 83 PHE 0.008 0.001 PHE A 692 TYR 0.011 0.001 TYR C 519 ARG 0.002 0.000 ARG D 861 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.6993 (m-10) cc_final: 0.6608 (m-80) REVERT: B 739 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8692 (pp30) REVERT: D 243 PHE cc_start: 0.7008 (m-10) cc_final: 0.6626 (m-80) REVERT: D 739 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8645 (pp30) outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 1.2684 time to fit residues: 176.5336 Evaluate side-chains 116 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 739 GLN Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 254 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 ASN A 840 ASN B 707 ASN C 840 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.090298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053260 restraints weight = 74786.154| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.69 r_work: 0.2775 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27344 Z= 0.253 Angle : 0.533 13.824 37212 Z= 0.275 Chirality : 0.044 0.186 4300 Planarity : 0.004 0.038 4840 Dihedral : 7.915 85.707 4072 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.77 % Allowed : 8.39 % Favored : 90.84 % 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: 0.06 (0.15), residues: 3468 helix: 0.71 (0.15), residues: 1316 sheet: 0.92 (0.21), residues: 584 loop : -0.84 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 278 HIS 0.002 0.001 HIS D 409 PHE 0.009 0.001 PHE A 855 TYR 0.014 0.001 TYR A 519 ARG 0.002 0.000 ARG A 719 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6582.51 seconds wall clock time: 119 minutes 16.78 seconds (7156.78 seconds total)