Starting phenix.real_space_refine (version: dev) on Wed Mar 15 01:28:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/03_2023/7duw_30869_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A ARG 673": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A ARG 784": "NH1" <-> "NH2" Residue "A ARG 798": "NH1" <-> "NH2" Residue "A ARG 806": "NH1" <-> "NH2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B ASP 559": "OD1" <-> "OD2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B ARG 673": "NH1" <-> "NH2" Residue "B ARG 756": "NH1" <-> "NH2" Residue "B GLU 775": "OE1" <-> "OE2" Residue "B ARG 784": "NH1" <-> "NH2" Residue "B ARG 798": "NH1" <-> "NH2" Residue "B ARG 806": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 13276 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6307 Classifications: {'peptide': 820} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 788} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6307 Classifications: {'peptide': 820} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 788} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 330 Unusual residues: {'EV9': 2, 'J4U': 1, 'LHG': 1, 'LMT': 1, 'PGT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 330 Unusual residues: {'EV9': 2, 'J4U': 1, 'LHG': 1, 'LMT': 1, 'PGT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG A 806 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 806 " occ=0.00 residue: pdb=" N ARG B 806 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 806 " occ=0.00 Time building chain proxies: 7.84, per 1000 atoms: 0.59 Number of scatterers: 13276 At special positions: 0 Unit cell: (131, 107, 109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 8 15.00 O 2370 8.00 N 2114 7.00 C 8744 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: 5.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 6 sheets defined 64.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 25 through 50 removed outlier: 3.569A pdb=" N ARG A 28 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA A 29 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 141 through 174 removed outlier: 6.191A pdb=" N ASP A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 221 through 245 Processing helix chain 'A' and resid 253 through 269 Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 293 through 324 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 335 through 364 Proline residue: A 345 - end of helix Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.667A pdb=" N TYR A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 407 removed outlier: 4.577A pdb=" N ARG A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 434 through 449 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 467 through 487 Processing helix chain 'A' and resid 495 through 498 removed outlier: 3.751A pdb=" N TRP A 498 " --> pdb=" O ASN A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 507 through 529 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 599 through 615 Proline residue: A 603 - end of helix Processing helix chain 'A' and resid 627 through 635 removed outlier: 4.702A pdb=" N SER A 631 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 673 removed outlier: 3.750A pdb=" N ALA A 662 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN A 663 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 687 through 703 removed outlier: 4.990A pdb=" N GLN A 692 " --> pdb=" O ASP A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 722 Processing helix chain 'A' and resid 765 through 780 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 807 through 818 Processing helix chain 'A' and resid 825 through 831 removed outlier: 3.879A pdb=" N PHE A 831 " --> pdb=" O PHE A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'B' and resid 25 through 50 removed outlier: 3.569A pdb=" N ARG B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA B 29 " --> pdb=" O ARG B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 141 through 174 removed outlier: 6.191A pdb=" N ASP B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 221 through 245 Processing helix chain 'B' and resid 253 through 269 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 293 through 324 Proline residue: B 311 - end of helix Processing helix chain 'B' and resid 335 through 364 Proline residue: B 345 - end of helix Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.666A pdb=" N TYR B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 407 removed outlier: 4.577A pdb=" N ARG B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 434 through 449 Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 467 through 487 Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.751A pdb=" N TRP B 498 " --> pdb=" O ASN B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 507 through 529 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 599 through 615 Proline residue: B 603 - end of helix Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.702A pdb=" N SER B 631 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 673 removed outlier: 3.750A pdb=" N ALA B 662 " --> pdb=" O GLY B 659 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN B 663 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 687 through 703 removed outlier: 4.991A pdb=" N GLN B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 765 through 780 Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'B' and resid 807 through 818 Processing helix chain 'B' and resid 825 through 831 removed outlier: 3.879A pdb=" N PHE B 831 " --> pdb=" O PHE B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 859 Processing sheet with id= A, first strand: chain 'A' and resid 569 through 572 removed outlier: 6.742A pdb=" N ARG A 619 " --> pdb=" O TRP A 589 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA A 591 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A 621 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 676 through 681 removed outlier: 6.058A pdb=" N LYS A 731 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 738 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 749 through 751 removed outlier: 6.355A pdb=" N ARG A 784 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA A 647 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET A 789 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 645 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG A 838 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU A 645 " --> pdb=" O GLN A 836 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN A 836 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA A 647 " --> pdb=" O GLU A 834 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU A 834 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 569 through 572 removed outlier: 6.742A pdb=" N ARG B 619 " --> pdb=" O TRP B 589 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA B 591 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 621 " --> pdb=" O ALA B 591 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 676 through 681 removed outlier: 6.059A pdb=" N LYS B 731 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE B 735 " --> pdb=" O LYS B 731 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 738 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 749 through 751 removed outlier: 6.355A pdb=" N ARG B 784 " --> pdb=" O GLY B 750 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA B 647 " --> pdb=" O LEU B 787 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 789 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU B 645 " --> pdb=" O MET B 789 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG B 838 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU B 645 " --> pdb=" O GLN B 836 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN B 836 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA B 647 " --> pdb=" O GLU B 834 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU B 834 " --> pdb=" O ALA B 647 " (cutoff:3.500A) 806 hydrogen bonds defined for protein. 2088 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: 4.70 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2002 1.31 - 1.43: 3659 1.43 - 1.56: 7807 1.56 - 1.68: 38 1.68 - 1.81: 70 Bond restraints: 13576 Sorted by residual: bond pdb=" C73 J4U B 901 " pdb=" O72 J4U B 901 " ideal model delta sigma weight residual 1.406 1.608 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C73 J4U A 906 " pdb=" O72 J4U A 906 " ideal model delta sigma weight residual 1.406 1.607 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C7 LHG A 904 " pdb=" O7 LHG A 904 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C11 PGT B 906 " pdb=" O3 PGT B 906 " ideal model delta sigma weight residual 1.327 1.451 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C7 LHG B 905 " pdb=" O7 LHG B 905 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 13571 not shown) Histogram of bond angle deviations from ideal: 98.23 - 106.50: 348 106.50 - 114.78: 8387 114.78 - 123.05: 9069 123.05 - 131.32: 562 131.32 - 139.60: 32 Bond angle restraints: 18398 Sorted by residual: angle pdb=" C06 EV9 B 903 " pdb=" C07 EV9 B 903 " pdb=" C08 EV9 B 903 " ideal model delta sigma weight residual 80.36 112.45 -32.09 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C06 EV9 A 902 " pdb=" C07 EV9 A 902 " pdb=" C08 EV9 A 902 " ideal model delta sigma weight residual 80.36 112.41 -32.05 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C06 EV9 B 904 " pdb=" C07 EV9 B 904 " pdb=" C08 EV9 B 904 " ideal model delta sigma weight residual 80.36 111.50 -31.14 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C06 EV9 A 903 " pdb=" C07 EV9 A 903 " pdb=" C08 EV9 A 903 " ideal model delta sigma weight residual 80.36 111.48 -31.12 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C74 J4U A 906 " pdb=" C73 J4U A 906 " pdb=" C76 J4U A 906 " ideal model delta sigma weight residual 116.65 139.60 -22.95 3.00e+00 1.11e-01 5.85e+01 ... (remaining 18393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.76: 7652 34.76 - 69.52: 174 69.52 - 104.28: 14 104.28 - 139.04: 4 139.04 - 173.80: 8 Dihedral angle restraints: 7852 sinusoidal: 3134 harmonic: 4718 Sorted by residual: dihedral pdb=" CA ILE A 686 " pdb=" C ILE A 686 " pdb=" N PRO A 687 " pdb=" CA PRO A 687 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ILE B 686 " pdb=" C ILE B 686 " pdb=" N PRO B 687 " pdb=" CA PRO B 687 " ideal model delta harmonic sigma weight residual -180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" C10 EV9 B 903 " pdb=" C11 EV9 B 903 " pdb=" C12 EV9 B 903 " pdb=" C13 EV9 B 903 " ideal model delta sinusoidal sigma weight residual 146.37 -27.43 173.80 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2104 0.116 - 0.231: 38 0.231 - 0.347: 8 0.347 - 0.463: 0 0.463 - 0.578: 2 Chirality restraints: 2152 Sorted by residual: chirality pdb=" C73 J4U B 901 " pdb=" C74 J4U B 901 " pdb=" O72 J4U B 901 " pdb=" O80 J4U B 901 " both_signs ideal model delta sigma weight residual False -2.55 -3.13 0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" C73 J4U A 906 " pdb=" C74 J4U A 906 " pdb=" O72 J4U A 906 " pdb=" O80 J4U A 906 " both_signs ideal model delta sigma weight residual False -2.55 -3.13 0.58 2.00e-01 2.50e+01 8.35e+00 chirality pdb=" C08 J4U B 901 " pdb=" C07 J4U B 901 " pdb=" C09 J4U B 901 " pdb=" C11 J4U B 901 " both_signs ideal model delta sigma weight residual False 2.34 2.63 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2149 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 J4U B 901 " -0.021 2.00e-02 2.50e+03 1.38e-01 2.38e+02 pdb=" C13 J4U B 901 " -0.054 2.00e-02 2.50e+03 pdb=" C14 J4U B 901 " -0.219 2.00e-02 2.50e+03 pdb=" C15 J4U B 901 " 0.167 2.00e-02 2.50e+03 pdb=" C16 J4U B 901 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 J4U A 906 " 0.021 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C13 J4U A 906 " 0.053 2.00e-02 2.50e+03 pdb=" C14 J4U A 906 " 0.219 2.00e-02 2.50e+03 pdb=" C15 J4U A 906 " -0.167 2.00e-02 2.50e+03 pdb=" C16 J4U A 906 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 175 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A 176 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.033 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 428 2.71 - 3.26: 14169 3.26 - 3.80: 23224 3.80 - 4.35: 29079 4.35 - 4.90: 48407 Nonbonded interactions: 115307 Sorted by model distance: nonbonded pdb=" O LEU B 465 " pdb=" OG1 THR B 466 " model vdw 2.162 2.440 nonbonded pdb=" O LEU A 465 " pdb=" OG1 THR A 466 " model vdw 2.163 2.440 nonbonded pdb=" OE1 GLU A 550 " pdb=" NH2 ARG A 553 " model vdw 2.199 2.520 nonbonded pdb=" OE1 GLU B 550 " pdb=" NH2 ARG B 553 " model vdw 2.199 2.520 nonbonded pdb=" OE1 GLU A 385 " pdb=" NH2 ARG A 512 " model vdw 2.256 2.520 ... (remaining 115302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 860 or resid 903)) selection = (chain 'B' and (resid 24 through 860 or resid 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 40 5.16 5 C 8744 2.51 5 N 2114 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.230 Check model and map are aligned: 0.200 Process input model: 38.730 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.008 0.202 13576 Z= 0.517 Angle : 1.018 32.089 18398 Z= 0.432 Chirality : 0.051 0.578 2152 Planarity : 0.006 0.138 2222 Dihedral : 16.612 173.802 4816 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.15 % 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: 1.16 (0.21), residues: 1628 helix: 1.46 (0.15), residues: 1096 sheet: -0.05 (0.45), residues: 142 loop : -0.79 (0.34), residues: 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.421 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 165 average time/residue: 1.3035 time to fit residues: 235.5159 Evaluate side-chains 101 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 13576 Z= 0.406 Angle : 0.687 8.739 18398 Z= 0.348 Chirality : 0.044 0.203 2152 Planarity : 0.006 0.057 2222 Dihedral : 14.528 171.099 2082 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 2.60 % 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: 0.74 (0.21), residues: 1628 helix: 1.11 (0.15), residues: 1100 sheet: -0.02 (0.46), residues: 114 loop : -0.89 (0.33), residues: 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 1.582 Fit side-chains outliers start: 34 outliers final: 14 residues processed: 132 average time/residue: 1.3661 time to fit residues: 197.0639 Evaluate side-chains 117 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.3273 time to fit residues: 2.8083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 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 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 13576 Z= 0.289 Angle : 0.611 9.247 18398 Z= 0.311 Chirality : 0.041 0.195 2152 Planarity : 0.006 0.058 2222 Dihedral : 12.880 174.870 2082 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1628 helix: 1.15 (0.15), residues: 1092 sheet: 0.19 (0.44), residues: 124 loop : -0.83 (0.34), residues: 412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 1.528 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 127 average time/residue: 1.2867 time to fit residues: 179.3504 Evaluate side-chains 107 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.8832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 42 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13576 Z= 0.233 Angle : 0.578 9.487 18398 Z= 0.294 Chirality : 0.041 0.185 2152 Planarity : 0.005 0.057 2222 Dihedral : 11.869 161.170 2082 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 2.52 % 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: 0.97 (0.21), residues: 1628 helix: 1.25 (0.16), residues: 1090 sheet: 0.43 (0.46), residues: 114 loop : -0.77 (0.34), residues: 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 1.393 Fit side-chains outliers start: 33 outliers final: 12 residues processed: 135 average time/residue: 1.2286 time to fit residues: 181.7810 Evaluate side-chains 111 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.4739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 13576 Z= 0.289 Angle : 0.602 9.831 18398 Z= 0.305 Chirality : 0.041 0.182 2152 Planarity : 0.005 0.056 2222 Dihedral : 11.768 153.541 2082 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 2.37 % 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: 0.95 (0.21), residues: 1628 helix: 1.24 (0.16), residues: 1088 sheet: 0.24 (0.42), residues: 132 loop : -0.73 (0.35), residues: 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 1.843 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 128 average time/residue: 1.3453 time to fit residues: 189.4252 Evaluate side-chains 105 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.9628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1751 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: