Starting phenix.real_space_refine on Thu Feb 15 20:25:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/02_2024/7duw_30869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/02_2024/7duw_30869.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/02_2024/7duw_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_30869/02_2024/7duw_30869_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/02_2024/7duw_30869_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/02_2024/7duw_30869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/02_2024/7duw_30869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/02_2024/7duw_30869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7duw_30869/02_2024/7duw_30869_updated.pdb" } resolution = 2.96 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= 0.000 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 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. 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-5238/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: 8.12, per 1000 atoms: 0.61 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: 5.39 Conformation dependent library (CDL) restraints added in 2.4 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: 3.29 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: 4.52 Time building geometry restraints manager: 5.76 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: 8118 34.76 - 69.52: 224 69.52 - 104.28: 34 104.28 - 139.04: 14 139.04 - 173.80: 8 Dihedral angle restraints: 8398 sinusoidal: 3680 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 8395 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 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: 1.630 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: 6.610 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.900 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 18.231 173.802 5362 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 % Allowed : 0.23 % Favored : 99.62 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 286 HIS 0.003 0.001 HIS A 814 PHE 0.020 0.002 PHE A 256 TYR 0.028 0.002 TYR B 88 ARG 0.008 0.001 ARG B 217 *********************** 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 : 1.504 Fit side-chains REVERT: A 417 THR cc_start: 0.8574 (m) cc_final: 0.8352 (m) REVERT: A 670 ARG cc_start: 0.7841 (tmm160) cc_final: 0.7509 (ttp80) REVERT: B 417 THR cc_start: 0.8575 (m) cc_final: 0.8345 (m) REVERT: B 670 ARG cc_start: 0.7842 (tmm160) cc_final: 0.7507 (ttp80) outliers start: 2 outliers final: 0 residues processed: 165 average time/residue: 1.2481 time to fit residues: 225.5808 Evaluate side-chains 100 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13576 Z= 0.410 Angle : 0.696 8.785 18398 Z= 0.350 Chirality : 0.045 0.197 2152 Planarity : 0.006 0.057 2222 Dihedral : 16.411 168.499 2628 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.60 % Allowed : 8.94 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1628 helix: 1.09 (0.15), residues: 1100 sheet: -0.03 (0.46), residues: 114 loop : -0.90 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 224 HIS 0.004 0.001 HIS B 832 PHE 0.024 0.002 PHE B 256 TYR 0.025 0.002 TYR B 88 ARG 0.005 0.001 ARG A 226 *********************** 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 149 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 1.330 Fit side-chains REVERT: A 379 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7728 (mm) REVERT: A 417 THR cc_start: 0.8446 (m) cc_final: 0.8241 (m) REVERT: A 743 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7782 (mtm) REVERT: B 379 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7729 (mm) REVERT: B 417 THR cc_start: 0.8448 (m) cc_final: 0.8241 (m) REVERT: B 743 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7797 (mtm) outliers start: 34 outliers final: 12 residues processed: 135 average time/residue: 1.2876 time to fit residues: 190.4000 Evaluate side-chains 121 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 TRP Chi-restraints excluded: chain B residue 734 LYS Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 813 GLU 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: 3.9990 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13576 Z= 0.346 Angle : 0.649 9.261 18398 Z= 0.326 Chirality : 0.043 0.257 2152 Planarity : 0.006 0.058 2222 Dihedral : 14.563 176.401 2628 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.14 % Allowed : 13.53 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1628 helix: 1.03 (0.15), residues: 1098 sheet: 0.08 (0.46), residues: 112 loop : -0.87 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 224 HIS 0.004 0.001 HIS B 832 PHE 0.021 0.002 PHE A 256 TYR 0.025 0.002 TYR B 88 ARG 0.004 0.000 ARG B 226 *********************** 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 133 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.473 Fit side-chains REVERT: A 30 LEU cc_start: 0.8520 (tm) cc_final: 0.8071 (tp) REVERT: A 379 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7609 (mm) REVERT: A 743 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7744 (mtm) REVERT: A 766 MET cc_start: 0.7573 (ttm) cc_final: 0.7364 (ttm) REVERT: B 30 LEU cc_start: 0.8489 (tm) cc_final: 0.8044 (tp) REVERT: B 379 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7603 (mm) REVERT: B 743 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7766 (mtm) outliers start: 28 outliers final: 10 residues processed: 124 average time/residue: 1.3434 time to fit residues: 182.0992 Evaluate side-chains 112 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 0.0670 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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** B 724 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13576 Z= 0.214 Angle : 0.574 9.463 18398 Z= 0.291 Chirality : 0.041 0.264 2152 Planarity : 0.005 0.057 2222 Dihedral : 13.179 163.787 2628 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.14 % Allowed : 16.67 % Favored : 81.19 % 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: 0.96 (0.21), residues: 1628 helix: 1.26 (0.16), residues: 1090 sheet: 0.36 (0.46), residues: 116 loop : -0.80 (0.34), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 804 HIS 0.003 0.001 HIS B 832 PHE 0.015 0.001 PHE A 256 TYR 0.026 0.002 TYR B 88 ARG 0.003 0.000 ARG B 670 *********************** 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 140 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.362 Fit side-chains REVERT: A 30 LEU cc_start: 0.8449 (tm) cc_final: 0.8190 (tm) REVERT: A 743 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7729 (mtm) REVERT: A 766 MET cc_start: 0.7563 (ttm) cc_final: 0.7359 (ttm) REVERT: A 798 ARG cc_start: 0.6568 (mmp80) cc_final: 0.5454 (tpp80) REVERT: A 853 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6967 (mtm) REVERT: B 30 LEU cc_start: 0.8441 (tm) cc_final: 0.8184 (tm) REVERT: B 743 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7732 (mtm) REVERT: B 798 ARG cc_start: 0.6539 (mmp80) cc_final: 0.5427 (tpp80) REVERT: B 853 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6982 (mtm) outliers start: 28 outliers final: 5 residues processed: 130 average time/residue: 1.2581 time to fit residues: 179.4737 Evaluate side-chains 104 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 853 MET 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: 0.9990 chunk 2 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 0.0270 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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: 0.7956 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13576 Z= 0.230 Angle : 0.581 9.820 18398 Z= 0.294 Chirality : 0.040 0.168 2152 Planarity : 0.005 0.056 2222 Dihedral : 12.783 163.476 2628 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.22 % Allowed : 18.04 % Favored : 79.74 % 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: 1.08 (0.22), residues: 1628 helix: 1.33 (0.16), residues: 1088 sheet: 0.35 (0.43), residues: 134 loop : -0.71 (0.35), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 804 HIS 0.003 0.001 HIS B 832 PHE 0.019 0.002 PHE B 503 TYR 0.024 0.002 TYR B 88 ARG 0.004 0.000 ARG A 553 *********************** 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 137 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.417 Fit side-chains REVERT: A 743 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7694 (mtm) REVERT: A 766 MET cc_start: 0.7577 (ttm) cc_final: 0.7340 (ttm) REVERT: A 798 ARG cc_start: 0.6339 (mmp80) cc_final: 0.5523 (tpp80) REVERT: A 853 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6890 (mtm) REVERT: B 379 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7679 (mm) REVERT: B 743 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7705 (mtm) REVERT: B 798 ARG cc_start: 0.6325 (mmp80) cc_final: 0.5509 (tpp80) REVERT: B 853 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6905 (mtm) outliers start: 29 outliers final: 7 residues processed: 131 average time/residue: 1.2059 time to fit residues: 174.2187 Evaluate side-chains 114 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 853 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 158 optimal weight: 0.0370 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 692 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13576 Z= 0.217 Angle : 0.570 10.063 18398 Z= 0.287 Chirality : 0.040 0.162 2152 Planarity : 0.005 0.056 2222 Dihedral : 12.496 162.674 2628 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.75 % Allowed : 18.88 % Favored : 78.36 % 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: 1.11 (0.22), residues: 1628 helix: 1.33 (0.16), residues: 1094 sheet: 0.47 (0.43), residues: 134 loop : -0.67 (0.36), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 804 HIS 0.002 0.001 HIS B 832 PHE 0.016 0.002 PHE A 256 TYR 0.033 0.002 TYR B 776 ARG 0.005 0.000 ARG B 553 *********************** REFINEMENT MACRO_CYCLE 6 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 148 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.573 Fit side-chains REVERT: A 743 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7706 (mtm) REVERT: A 798 ARG cc_start: 0.6129 (mmp80) cc_final: 0.5309 (tpp80) REVERT: A 853 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6896 (mtm) REVERT: B 743 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7723 (mtm) REVERT: B 853 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6869 (mtm) outliers start: 36 outliers final: 11 residues processed: 138 average time/residue: 1.2565 time to fit residues: 192.2902 Evaluate side-chains 115 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 TRP Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 853 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 115 optimal weight: 0.2980 chunk 89 optimal weight: 0.0870 chunk 133 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.7933 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13576 Z= 0.203 Angle : 0.566 10.248 18398 Z= 0.285 Chirality : 0.040 0.172 2152 Planarity : 0.005 0.055 2222 Dihedral : 12.284 163.583 2628 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.06 % Allowed : 20.18 % Favored : 77.75 % 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: 1.14 (0.22), residues: 1628 helix: 1.34 (0.16), residues: 1098 sheet: 0.55 (0.44), residues: 134 loop : -0.68 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 804 HIS 0.002 0.001 HIS A 832 PHE 0.016 0.001 PHE A 256 TYR 0.031 0.002 TYR A 776 ARG 0.010 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 7 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 139 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.459 Fit side-chains REVERT: A 276 PHE cc_start: 0.8300 (t80) cc_final: 0.7921 (t80) REVERT: A 743 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7710 (mtm) REVERT: A 798 ARG cc_start: 0.5904 (mmp80) cc_final: 0.5272 (tpp80) REVERT: A 853 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6855 (mtm) REVERT: B 276 PHE cc_start: 0.8352 (t80) cc_final: 0.7957 (t80) REVERT: B 743 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7727 (mtm) REVERT: B 798 ARG cc_start: 0.6315 (mmp80) cc_final: 0.5256 (tpp80) REVERT: B 853 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6873 (mtm) outliers start: 27 outliers final: 9 residues processed: 128 average time/residue: 1.1485 time to fit residues: 162.9108 Evaluate side-chains 117 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 TRP Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 853 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.0070 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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: 0.7922 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13576 Z= 0.193 Angle : 0.564 10.314 18398 Z= 0.284 Chirality : 0.040 0.173 2152 Planarity : 0.005 0.055 2222 Dihedral : 12.126 166.382 2628 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.52 % Allowed : 20.18 % Favored : 77.29 % 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: 1.22 (0.22), residues: 1628 helix: 1.39 (0.16), residues: 1102 sheet: 0.60 (0.44), residues: 134 loop : -0.67 (0.36), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 804 HIS 0.002 0.001 HIS B 814 PHE 0.016 0.001 PHE B 256 TYR 0.027 0.002 TYR A 776 ARG 0.012 0.001 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 8 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 147 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.431 Fit side-chains REVERT: A 276 PHE cc_start: 0.8367 (t80) cc_final: 0.8038 (t80) REVERT: A 795 MET cc_start: 0.6590 (ttm) cc_final: 0.6359 (ttt) REVERT: A 798 ARG cc_start: 0.5775 (mmp80) cc_final: 0.5163 (tpp80) REVERT: A 853 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6955 (mtp) REVERT: B 276 PHE cc_start: 0.8365 (t80) cc_final: 0.8005 (t80) REVERT: B 795 MET cc_start: 0.6544 (ttm) cc_final: 0.6322 (ttt) REVERT: B 798 ARG cc_start: 0.6244 (mmp80) cc_final: 0.5174 (tpp80) REVERT: B 853 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6958 (mtp) outliers start: 33 outliers final: 10 residues processed: 136 average time/residue: 1.1362 time to fit residues: 171.2787 Evaluate side-chains 118 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 TRP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 853 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 0.0060 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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: 0.7944 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13576 Z= 0.233 Angle : 0.580 10.583 18398 Z= 0.292 Chirality : 0.041 0.199 2152 Planarity : 0.005 0.055 2222 Dihedral : 12.230 166.975 2628 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.83 % Allowed : 21.18 % Favored : 76.99 % 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: 1.14 (0.22), residues: 1628 helix: 1.37 (0.16), residues: 1096 sheet: 0.51 (0.44), residues: 134 loop : -0.76 (0.35), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 224 HIS 0.003 0.001 HIS B 814 PHE 0.019 0.002 PHE A 256 TYR 0.027 0.002 TYR B 776 ARG 0.012 0.001 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 9 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 136 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.395 Fit side-chains REVERT: A 276 PHE cc_start: 0.8395 (t80) cc_final: 0.8008 (t80) REVERT: A 743 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7702 (mtm) REVERT: A 795 MET cc_start: 0.6575 (ttm) cc_final: 0.6327 (ttt) REVERT: A 853 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6969 (mtp) REVERT: B 276 PHE cc_start: 0.8409 (t80) cc_final: 0.8001 (t80) REVERT: B 743 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7680 (mtm) REVERT: B 798 ARG cc_start: 0.6198 (mmp80) cc_final: 0.5086 (tpp80) REVERT: B 853 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6979 (mtp) outliers start: 24 outliers final: 12 residues processed: 126 average time/residue: 1.1764 time to fit residues: 164.8885 Evaluate side-chains 122 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 TRP Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 853 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.7980 chunk 155 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7942 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13576 Z= 0.232 Angle : 0.587 10.747 18398 Z= 0.295 Chirality : 0.041 0.208 2152 Planarity : 0.005 0.057 2222 Dihedral : 12.203 166.005 2628 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.61 % Allowed : 22.25 % Favored : 76.15 % 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: 1.17 (0.21), residues: 1628 helix: 1.39 (0.16), residues: 1092 sheet: 0.49 (0.45), residues: 134 loop : -0.73 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 804 HIS 0.003 0.001 HIS B 814 PHE 0.018 0.002 PHE A 256 TYR 0.024 0.002 TYR A 88 ARG 0.013 0.001 ARG A 553 ********************** REFINEMENT MACRO_CYCLE 10 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 132 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.555 Fit side-chains REVERT: A 276 PHE cc_start: 0.8395 (t80) cc_final: 0.7995 (t80) REVERT: A 795 MET cc_start: 0.6557 (ttm) cc_final: 0.6317 (ttt) REVERT: A 853 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6972 (mtp) REVERT: B 276 PHE cc_start: 0.8401 (t80) cc_final: 0.7987 (t80) REVERT: B 798 ARG cc_start: 0.6115 (mmp80) cc_final: 0.5056 (tpp80) REVERT: B 853 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6979 (mtp) outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 1.2953 time to fit residues: 177.7431 Evaluate side-chains 114 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 TRP Chi-restraints excluded: chain B residue 853 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 119 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099649 restraints weight = 18320.391| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.78 r_work: 0.3041 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13576 Z= 0.231 Angle : 0.604 10.648 18398 Z= 0.304 Chirality : 0.041 0.209 2152 Planarity : 0.005 0.057 2222 Dihedral : 12.164 165.567 2628 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.68 % Allowed : 22.40 % Favored : 75.92 % 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: 1.17 (0.21), residues: 1628 helix: 1.40 (0.16), residues: 1092 sheet: 0.40 (0.45), residues: 134 loop : -0.71 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 804 HIS 0.002 0.001 HIS B 814 PHE 0.018 0.002 PHE A 256 TYR 0.025 0.002 TYR B 776 ARG 0.012 0.001 ARG A 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4110.62 seconds wall clock time: 74 minutes 14.53 seconds (4454.53 seconds total)