Starting phenix.real_space_refine on Sat Aug 8 10:06:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9r_71420/08_2026/9p9r_71420_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9r_71420/08_2026/9p9r_71420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9r_71420/08_2026/9p9r_71420_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9r_71420/08_2026/9p9r_71420_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9r_71420/08_2026/9p9r_71420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9r_71420/08_2026/9p9r_71420.map" } resolution = 3.14 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 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= 0.047 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 S 72 5.16 5 C 8423 2.51 5 N 2375 2.21 5 O 2691 1.98 5 H 12894 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26455 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 4959 Classifications: {'peptide': 326} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Chain: "B" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2666 Classifications: {'peptide': 169} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 168} Chain: "C" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4952 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 1 Chain: "D" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2668 Classifications: {'peptide': 169} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 168} Chain: "E" Number of atoms: 4950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4950 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 1 Chain: "F" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2666 Classifications: {'peptide': 169} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 168} Chain: "H" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1694 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1732 Classifications: {'peptide': 113} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.27, per 1000 atoms: 0.16 Number of scatterers: 26455 At special positions: 0 Unit cell: (86.632, 84.966, 184.093, 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 72 16.00 O 2691 8.00 N 2375 7.00 C 8423 6.00 H 12894 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS D 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 324 " distance=2.03 Simple disulfide: pdb=" SG CYS D 493 " - pdb=" SG CYS D 497 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS F 486 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 296 " distance=2.03 Simple disulfide: pdb=" SG CYS E 72 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 300 " - pdb=" SG CYS E 324 " distance=2.02 Simple disulfide: pdb=" SG CYS F 493 " - pdb=" SG CYS F 497 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 46 " " NAG A 402 " - " ASN A 174 " " NAG B 601 " - " ASN B 431 " " NAG B 602 " - " ASN B 507 " " NAG B 603 " - " ASN B 503 " " NAG D 601 " - " ASN D 431 " " NAG D 603 " - " ASN D 503 " " NAG E 401 " - " ASN E 174 " " NAG F 601 " - " ASN F 431 " " NAG F 602 " - " ASN F 507 " " NAG F 603 " - " ASN F 503 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 962.2 milliseconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3118 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 41 sheets defined 23.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.865A pdb=" N ILE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.873A pdb=" N GLU A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'B' and resid 386 through 406 removed outlier: 3.647A pdb=" N LYS B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 475 Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 507 through 510 Processing helix chain 'B' and resid 511 through 521 removed outlier: 3.506A pdb=" N ILE B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.744A pdb=" N ILE C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.419A pdb=" N GLU C 89 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 90 " --> pdb=" O HIS C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 90' Processing helix chain 'C' and resid 112 through 122 removed outlier: 3.541A pdb=" N GLU C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 196 through 205 Processing helix chain 'D' and resid 386 through 400 removed outlier: 3.908A pdb=" N LYS D 400 " --> pdb=" O GLN D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 476 Processing helix chain 'D' and resid 494 through 504 Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 512 through 521 Processing helix chain 'E' and resid 75 through 80 removed outlier: 3.924A pdb=" N ILE E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.983A pdb=" N LEU E 88 " --> pdb=" O ASP E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.765A pdb=" N GLU E 122 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 205 Processing helix chain 'F' and resid 386 through 406 removed outlier: 3.581A pdb=" N LYS F 400 " --> pdb=" O GLN F 396 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU F 404 " --> pdb=" O LYS F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 476 Processing helix chain 'F' and resid 494 through 504 Processing helix chain 'F' and resid 507 through 510 Processing helix chain 'F' and resid 511 through 521 removed outlier: 3.528A pdb=" N ASN F 518 " --> pdb=" O GLU F 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.893A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.568A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG L 83 " --> pdb=" O GLY L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.723A pdb=" N GLU B 480 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 25 removed outlier: 3.716A pdb=" N GLY A 24 " --> pdb=" O GLY B 372 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 372 " --> pdb=" O GLY A 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 3.712A pdb=" N GLU A 52 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.826A pdb=" N VAL A 59 " --> pdb=" O ASP A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.433A pdb=" N VAL A 67 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 108 through 110 removed outlier: 7.976A pdb=" N VAL A 188 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 126 through 130 Processing sheet with id=AB1, first strand: chain 'A' and resid 173 through 178 removed outlier: 3.530A pdb=" N PHE A 256 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AB3, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.521A pdb=" N GLU D 480 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 32 through 35 Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.760A pdb=" N VAL C 59 " --> pdb=" O ASP C 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 66 through 68 Processing sheet with id=AB9, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.881A pdb=" N ARG C 109 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N TRP C 243 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL C 188 " --> pdb=" O PRO C 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AC2, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.559A pdb=" N VAL C 252 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 255 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC4, first strand: chain 'D' and resid 372 through 373 Processing sheet with id=AC5, first strand: chain 'D' and resid 376 through 377 removed outlier: 4.031A pdb=" N ASN D 377 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 380 " --> pdb=" O ASN D 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 381 through 385 removed outlier: 3.707A pdb=" N PHE F 373 " --> pdb=" O ALA F 384 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY E 24 " --> pdb=" O GLY F 372 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU F 480 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 32 through 34 Processing sheet with id=AC8, first strand: chain 'E' and resid 47 through 49 removed outlier: 3.617A pdb=" N THR E 48 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 59 Processing sheet with id=AD2, first strand: chain 'E' and resid 67 through 69 removed outlier: 6.465A pdb=" N ILE E 95 " --> pdb=" O ILE E 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 108 through 110 removed outlier: 6.445A pdb=" N VAL E 188 " --> pdb=" O ARG E 265 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG E 265 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 108 through 110 removed outlier: 8.124A pdb=" N VAL E 188 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 144 through 148 removed outlier: 4.702A pdb=" N CYS E 147 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 176 through 178 removed outlier: 3.562A pdb=" N GLY E 214 " --> pdb=" O THR E 253 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR E 218 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.739A pdb=" N MET H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET H 80 " --> pdb=" O MET H 20 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 33 through 35 removed outlier: 3.931A pdb=" N TRP H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AE1, first strand: chain 'H' and resid 49 through 50 Processing sheet with id=AE2, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AE3, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.109A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.592A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR L 97 " --> pdb=" O ASN L 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.592A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12894 1.03 - 1.23: 120 1.23 - 1.43: 5802 1.43 - 1.62: 7793 1.62 - 1.82: 104 Bond restraints: 26713 Sorted by residual: bond pdb=" N GLN A 168 " pdb=" CA GLN A 168 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.20e-02 6.94e+03 9.54e+00 bond pdb=" CA GLN A 168 " pdb=" C GLN A 168 " ideal model delta sigma weight residual 1.520 1.548 -0.028 1.20e-02 6.94e+03 5.44e+00 bond pdb=" N GLN A 168 " pdb=" H GLN A 168 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C ASN A 167 " pdb=" N GLN A 168 " ideal model delta sigma weight residual 1.331 1.351 -0.020 1.30e-02 5.92e+03 2.27e+00 bond pdb=" C GLN A 168 " pdb=" O GLN A 168 " ideal model delta sigma weight residual 1.234 1.218 0.016 1.15e-02 7.56e+03 2.01e+00 ... (remaining 26708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 47123 1.67 - 3.34: 764 3.34 - 5.01: 78 5.01 - 6.68: 6 6.68 - 8.35: 1 Bond angle restraints: 47972 Sorted by residual: angle pdb=" C GLN A 168 " pdb=" CA GLN A 168 " pdb=" CB GLN A 168 " ideal model delta sigma weight residual 109.80 118.15 -8.35 1.70e+00 3.46e-01 2.41e+01 angle pdb=" N GLN A 168 " pdb=" CA GLN A 168 " pdb=" CB GLN A 168 " ideal model delta sigma weight residual 110.71 105.77 4.94 1.66e+00 3.63e-01 8.84e+00 angle pdb=" C ARG F 476 " pdb=" CA ARG F 476 " pdb=" CB ARG F 476 " ideal model delta sigma weight residual 116.34 112.35 3.99 1.40e+00 5.10e-01 8.13e+00 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.94 3.23 1.14e+00 7.69e-01 8.04e+00 angle pdb=" CA GLN A 168 " pdb=" C GLN A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 116.29 120.10 -3.81 1.45e+00 4.76e-01 6.92e+00 ... (remaining 47967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 11661 17.18 - 34.35: 861 34.35 - 51.53: 209 51.53 - 68.71: 72 68.71 - 85.88: 6 Dihedral angle restraints: 12809 sinusoidal: 7110 harmonic: 5699 Sorted by residual: dihedral pdb=" CB CYS B 493 " pdb=" SG CYS B 493 " pdb=" SG CYS B 497 " pdb=" CB CYS B 497 " ideal model delta sinusoidal sigma weight residual 93.00 133.14 -40.14 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CB CYS D 493 " pdb=" SG CYS D 493 " pdb=" SG CYS D 497 " pdb=" CB CYS D 497 " ideal model delta sinusoidal sigma weight residual 93.00 132.39 -39.39 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" CA ARG D 374 " pdb=" C ARG D 374 " pdb=" N HIS D 375 " pdb=" CA HIS D 375 " ideal model delta harmonic sigma weight residual -180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 12806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1329 0.034 - 0.068: 523 0.068 - 0.102: 107 0.102 - 0.136: 70 0.136 - 0.171: 11 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE E 239 " pdb=" N ILE E 239 " pdb=" C ILE E 239 " pdb=" CB ILE E 239 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE A 211 " pdb=" N ILE A 211 " pdb=" C ILE A 211 " pdb=" CB ILE A 211 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 2037 not shown) Planarity restraints: 4104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " -0.326 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG B 601 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " -0.084 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " 0.505 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 431 " 0.101 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" CG ASN B 431 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 431 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 431 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG B 601 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 168 " 0.096 2.00e-02 2.50e+03 1.02e-01 1.58e+02 pdb=" CD GLN A 168 " -0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN A 168 " -0.093 2.00e-02 2.50e+03 pdb=" NE2 GLN A 168 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 168 " -0.149 2.00e-02 2.50e+03 pdb="HE22 GLN A 168 " 0.151 2.00e-02 2.50e+03 ... (remaining 4101 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.49: 18253 2.49 - 3.02: 59152 3.02 - 3.54: 66411 3.54 - 4.07: 91143 4.07 - 4.60: 132000 Nonbonded interactions: 366959 Sorted by model distance: nonbonded pdb=" H GLN E 83 " pdb=" H CYS E 84 " model vdw 1.962 2.100 nonbonded pdb=" H PHE H 100B" pdb=" HH TYR L 36 " model vdw 1.968 2.100 nonbonded pdb="HH21 ARG A 229 " pdb=" HG1 THR E 212 " model vdw 1.971 2.100 nonbonded pdb=" H ARG C 149 " pdb=" HG SER C 153 " model vdw 1.973 2.100 nonbonded pdb=" H ASP E 264 " pdb=" H ARG E 265 " model vdw 1.984 2.100 ... (remaining 366954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 274 or resid 278 through 346)) selection = (chain 'C' and (resid 19 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA o \ r name HB2 or name HB3)) or resid 47 through 173 or (resid 174 and (name N or na \ me CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name \ H or name HA or name HB2 or name HB3)) or resid 175 through 346)) selection = (chain 'E' and (resid 19 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA o \ r name HB2 or name HB3)) or resid 47 through 346)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 353 through 506 or (resid 507 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3)) or resid 508 through 603)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.320 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: 0.130 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.910 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.003 0.037 13850 Z= 0.150 Angle : 0.581 8.758 18743 Z= 0.312 Chirality : 0.042 0.171 2040 Planarity : 0.007 0.284 2451 Dihedral : 11.166 85.882 5298 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.34 % Allowed : 2.68 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.20), residues: 1689 helix: 2.17 (0.28), residues: 338 sheet: -2.60 (0.27), residues: 291 loop : -1.91 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.014 0.001 TYR H 100A PHE 0.012 0.001 PHE D 373 TRP 0.006 0.001 TRP H 47 HIS 0.006 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (13819) covalent geometry : angle 0.57140 / 0.31 (18670) SS BOND : bond 0.00344 / 0.18 ( 20) SS BOND : angle 1.05116 / 0.59 ( 40) hydrogen bonds : bond 0.20847 / 13.89 ( 446) hydrogen bonds : angle 7.97643 / 5.51 ( 1263) link_NAG-ASN : bond 0.00304 / 0.19 ( 11) link_NAG-ASN : angle 2.42521 / 1.56 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 299 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 388 LYS cc_start: 0.8562 (tttt) cc_final: 0.8343 (mttt) REVERT: B 464 MET cc_start: 0.8542 (tpt) cc_final: 0.7964 (tpt) REVERT: C 22 CYS cc_start: 0.7511 (m) cc_final: 0.7232 (m) REVERT: C 58 LYS cc_start: 0.7222 (mttt) cc_final: 0.6946 (mttm) REVERT: C 161 LEU cc_start: 0.9131 (mp) cc_final: 0.8930 (mp) REVERT: D 368 ASP cc_start: 0.8669 (p0) cc_final: 0.8393 (p0) REVERT: E 127 ASP cc_start: 0.8494 (t0) cc_final: 0.8174 (t0) REVERT: E 261 ILE cc_start: 0.8853 (mm) cc_final: 0.8646 (mt) REVERT: H 13 ARG cc_start: 0.7313 (mmp80) cc_final: 0.6889 (mmm160) REVERT: H 32 TYR cc_start: 0.7280 (m-80) cc_final: 0.7041 (m-80) outliers start: 5 outliers final: 2 residues processed: 304 average time/residue: 0.2790 time to fit residues: 121.3558 Evaluate side-chains 204 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain F residue 493 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 ASN D 455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118827 restraints weight = 61435.132| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.51 r_work: 0.3394 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13850 Z= 0.159 Angle : 0.508 7.569 18743 Z= 0.274 Chirality : 0.041 0.509 2040 Planarity : 0.004 0.054 2451 Dihedral : 5.261 58.883 2104 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.03 % Allowed : 7.57 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.20), residues: 1689 helix: 2.35 (0.27), residues: 338 sheet: -2.38 (0.27), residues: 304 loop : -1.88 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 492 TYR 0.012 0.001 TYR D 468 PHE 0.013 0.001 PHE L 49 TRP 0.007 0.001 TRP E 243 HIS 0.004 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (13819) covalent geometry : angle 0.50190 / 0.27 (18670) SS BOND : bond 0.00284 / 0.16 ( 20) SS BOND : angle 0.83482 / 0.55 ( 40) hydrogen bonds : bond 0.05052 / 3.38 ( 446) hydrogen bonds : angle 5.78965 / 4.04 ( 1263) link_NAG-ASN : bond 0.00161 / 0.09 ( 11) link_NAG-ASN : angle 1.82062 / 1.23 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 464 MET cc_start: 0.8498 (tpt) cc_final: 0.7888 (tpt) REVERT: C 22 CYS cc_start: 0.7360 (m) cc_final: 0.7096 (m) REVERT: C 161 LEU cc_start: 0.9130 (mp) cc_final: 0.8903 (mp) REVERT: D 368 ASP cc_start: 0.8666 (p0) cc_final: 0.8388 (p0) REVERT: D 451 MET cc_start: 0.8237 (tpt) cc_final: 0.7999 (ptp) REVERT: E 127 ASP cc_start: 0.8468 (t0) cc_final: 0.8176 (t0) REVERT: E 261 ILE cc_start: 0.8863 (mm) cc_final: 0.8620 (mt) REVERT: H 13 ARG cc_start: 0.7329 (mmp80) cc_final: 0.6931 (mmm160) outliers start: 15 outliers final: 9 residues processed: 211 average time/residue: 0.2556 time to fit residues: 79.4448 Evaluate side-chains 197 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 493 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 ASN B 491 HIS B 496 GLN D 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118110 restraints weight = 61340.608| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.45 r_work: 0.3387 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13850 Z= 0.140 Angle : 0.475 6.222 18743 Z= 0.254 Chirality : 0.040 0.221 2040 Planarity : 0.003 0.050 2451 Dihedral : 5.127 57.122 2104 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.24 % Allowed : 8.26 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.20), residues: 1689 helix: 2.42 (0.27), residues: 338 sheet: -2.25 (0.27), residues: 303 loop : -1.89 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 492 TYR 0.013 0.001 TYR H 100A PHE 0.009 0.001 PHE L 49 TRP 0.008 0.001 TRP A 160 HIS 0.004 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (13819) covalent geometry : angle 0.46856 / 0.25 (18670) SS BOND : bond 0.00647 / 0.44 ( 20) SS BOND : angle 0.93320 / 0.68 ( 40) hydrogen bonds : bond 0.04507 / 3.01 ( 446) hydrogen bonds : angle 5.36687 / 3.75 ( 1263) link_NAG-ASN : bond 0.00181 / 0.11 ( 11) link_NAG-ASN : angle 1.71495 / 1.14 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 GLN cc_start: 0.8601 (tt0) cc_final: 0.8362 (tt0) REVERT: B 388 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8473 (ttmt) REVERT: B 464 MET cc_start: 0.8520 (tpt) cc_final: 0.7896 (tpt) REVERT: C 22 CYS cc_start: 0.7369 (m) cc_final: 0.7147 (m) REVERT: C 161 LEU cc_start: 0.9102 (mp) cc_final: 0.8890 (mp) REVERT: D 368 ASP cc_start: 0.8666 (p0) cc_final: 0.8377 (p0) REVERT: D 451 MET cc_start: 0.8214 (tpt) cc_final: 0.8000 (ptp) REVERT: E 127 ASP cc_start: 0.8496 (t0) cc_final: 0.8133 (t0) REVERT: E 261 ILE cc_start: 0.8871 (mm) cc_final: 0.8603 (mt) REVERT: H 13 ARG cc_start: 0.7210 (mmp80) cc_final: 0.6910 (mmm160) REVERT: L 55 GLU cc_start: 0.5381 (OUTLIER) cc_final: 0.4873 (pm20) REVERT: L 91 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6043 (p90) outliers start: 18 outliers final: 13 residues processed: 207 average time/residue: 0.2408 time to fit residues: 74.4752 Evaluate side-chains 202 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 104 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 131 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 ASN F 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117949 restraints weight = 61624.840| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.35 r_work: 0.3386 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13850 Z= 0.129 Angle : 0.459 4.983 18743 Z= 0.245 Chirality : 0.039 0.164 2040 Planarity : 0.003 0.044 2451 Dihedral : 5.120 57.672 2104 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.58 % Allowed : 8.81 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1689 helix: 2.47 (0.27), residues: 338 sheet: -2.14 (0.28), residues: 307 loop : -1.87 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 492 TYR 0.009 0.001 TYR D 468 PHE 0.009 0.001 PHE L 49 TRP 0.006 0.001 TRP A 160 HIS 0.004 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13819) covalent geometry : angle 0.45294 / 0.24 (18670) SS BOND : bond 0.00302 / 0.19 ( 20) SS BOND : angle 0.66296 / 0.46 ( 40) hydrogen bonds : bond 0.04176 / 2.79 ( 446) hydrogen bonds : angle 5.07622 / 3.56 ( 1263) link_NAG-ASN : bond 0.00174 / 0.10 ( 11) link_NAG-ASN : angle 1.67549 / 1.09 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 MET cc_start: 0.7887 (ptt) cc_final: 0.7687 (ptt) REVERT: B 388 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8366 (mttt) REVERT: C 161 LEU cc_start: 0.9084 (mp) cc_final: 0.8871 (mp) REVERT: D 368 ASP cc_start: 0.8676 (p0) cc_final: 0.8359 (p0) REVERT: E 261 ILE cc_start: 0.8852 (mm) cc_final: 0.8592 (mt) REVERT: H 13 ARG cc_start: 0.7234 (mmp80) cc_final: 0.6917 (mmm160) REVERT: L 55 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5302 (pm20) outliers start: 23 outliers final: 17 residues processed: 203 average time/residue: 0.2172 time to fit residues: 66.7769 Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 143 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 402 ASN D 428 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114385 restraints weight = 63109.265| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.34 r_work: 0.3333 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13850 Z= 0.194 Angle : 0.496 5.344 18743 Z= 0.266 Chirality : 0.040 0.172 2040 Planarity : 0.003 0.043 2451 Dihedral : 5.337 57.214 2104 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.72 % Allowed : 9.36 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.20), residues: 1689 helix: 2.31 (0.27), residues: 338 sheet: -2.17 (0.28), residues: 307 loop : -1.98 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 229 TYR 0.012 0.002 TYR D 468 PHE 0.010 0.001 PHE F 373 TRP 0.008 0.001 TRP A 160 HIS 0.004 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (13819) covalent geometry : angle 0.49009 / 0.26 (18670) SS BOND : bond 0.00371 / 0.19 ( 20) SS BOND : angle 0.82655 / 0.58 ( 40) hydrogen bonds : bond 0.04314 / 2.89 ( 446) hydrogen bonds : angle 5.02885 / 3.52 ( 1263) link_NAG-ASN : bond 0.00288 / 0.17 ( 11) link_NAG-ASN : angle 1.81215 / 1.17 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 MET cc_start: 0.7847 (ptt) cc_final: 0.7636 (ptt) REVERT: H 13 ARG cc_start: 0.7255 (mmp80) cc_final: 0.6939 (mmm160) REVERT: L 55 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5372 (pm20) outliers start: 25 outliers final: 18 residues processed: 201 average time/residue: 0.2281 time to fit residues: 69.7599 Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 428 ASN E 25 HIS E 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116239 restraints weight = 62716.248| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.32 r_work: 0.3339 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13850 Z= 0.140 Angle : 0.466 4.526 18743 Z= 0.250 Chirality : 0.040 0.162 2040 Planarity : 0.003 0.042 2451 Dihedral : 5.296 57.232 2104 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.86 % Allowed : 9.64 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.20), residues: 1689 helix: 2.46 (0.28), residues: 332 sheet: -2.09 (0.28), residues: 312 loop : -1.97 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 98 TYR 0.010 0.001 TYR D 468 PHE 0.008 0.001 PHE D 373 TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (13819) covalent geometry : angle 0.45979 / 0.25 (18670) SS BOND : bond 0.00356 / 0.19 ( 20) SS BOND : angle 0.96478 / 0.71 ( 40) hydrogen bonds : bond 0.04077 / 2.73 ( 446) hydrogen bonds : angle 4.88944 / 3.43 ( 1263) link_NAG-ASN : bond 0.00191 / 0.11 ( 11) link_NAG-ASN : angle 1.68990 / 1.08 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 388 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8305 (mtmt) REVERT: E 26 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.7352 (p-80) REVERT: H 13 ARG cc_start: 0.7266 (mmp80) cc_final: 0.6962 (mmm160) REVERT: L 55 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5446 (pm20) outliers start: 27 outliers final: 20 residues processed: 199 average time/residue: 0.2299 time to fit residues: 69.4706 Evaluate side-chains 198 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 HIS D 428 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113476 restraints weight = 63169.953| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.32 r_work: 0.3319 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 13850 Z= 0.200 Angle : 0.511 8.285 18743 Z= 0.273 Chirality : 0.041 0.233 2040 Planarity : 0.003 0.041 2451 Dihedral : 5.424 56.783 2104 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.13 % Allowed : 9.70 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.19), residues: 1689 helix: 2.29 (0.27), residues: 338 sheet: -2.10 (0.28), residues: 306 loop : -2.05 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.013 0.002 TYR D 468 PHE 0.011 0.001 PHE D 373 TRP 0.008 0.001 TRP A 160 HIS 0.005 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (13819) covalent geometry : angle 0.49921 / 0.27 (18670) SS BOND : bond 0.00504 / 0.26 ( 20) SS BOND : angle 1.81218 / 1.02 ( 40) hydrogen bonds : bond 0.04262 / 2.85 ( 446) hydrogen bonds : angle 4.91289 / 3.44 ( 1263) link_NAG-ASN : bond 0.00306 / 0.18 ( 11) link_NAG-ASN : angle 1.80319 / 1.16 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 388 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8323 (mtmt) REVERT: E 26 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.7295 (p-80) REVERT: H 13 ARG cc_start: 0.7296 (mmp80) cc_final: 0.6960 (mmm160) REVERT: H 54 ASN cc_start: 0.7635 (m110) cc_final: 0.7362 (m110) REVERT: L 55 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5518 (pm20) outliers start: 31 outliers final: 26 residues processed: 197 average time/residue: 0.2327 time to fit residues: 69.2047 Evaluate side-chains 198 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 106 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115659 restraints weight = 62861.897| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.33 r_work: 0.3346 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 13850 Z= 0.122 Angle : 0.485 13.584 18743 Z= 0.256 Chirality : 0.039 0.186 2040 Planarity : 0.003 0.042 2451 Dihedral : 5.291 58.919 2104 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.65 % Allowed : 10.53 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.20), residues: 1689 helix: 2.51 (0.27), residues: 332 sheet: -1.92 (0.28), residues: 322 loop : -1.95 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 519 TYR 0.009 0.001 TYR D 468 PHE 0.008 0.001 PHE D 373 TRP 0.006 0.001 TRP H 47 HIS 0.006 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (13819) covalent geometry : angle 0.46859 / 0.25 (18670) SS BOND : bond 0.00730 / 0.39 ( 20) SS BOND : angle 2.35161 / 1.40 ( 40) hydrogen bonds : bond 0.03945 / 2.63 ( 446) hydrogen bonds : angle 4.76494 / 3.34 ( 1263) link_NAG-ASN : bond 0.00165 / 0.10 ( 11) link_NAG-ASN : angle 1.62373 / 1.03 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 388 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8343 (mtmt) REVERT: E 26 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.7361 (p-80) REVERT: H 13 ARG cc_start: 0.7310 (mmp80) cc_final: 0.6971 (mmm160) REVERT: H 54 ASN cc_start: 0.7496 (m110) cc_final: 0.7246 (m110) REVERT: L 55 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.5247 (pm20) outliers start: 24 outliers final: 20 residues processed: 194 average time/residue: 0.2418 time to fit residues: 71.7594 Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113177 restraints weight = 63393.360| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.34 r_work: 0.3315 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 13850 Z= 0.196 Angle : 0.521 13.034 18743 Z= 0.276 Chirality : 0.040 0.169 2040 Planarity : 0.003 0.040 2451 Dihedral : 5.435 56.312 2104 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.86 % Allowed : 10.74 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.20), residues: 1689 helix: 2.38 (0.28), residues: 332 sheet: -2.08 (0.28), residues: 312 loop : -2.00 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.012 0.002 TYR D 468 PHE 0.012 0.001 PHE D 373 TRP 0.007 0.001 TRP A 160 HIS 0.004 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (13819) covalent geometry : angle 0.50576 / 0.27 (18670) SS BOND : bond 0.00584 / 0.30 ( 20) SS BOND : angle 2.25191 / 1.35 ( 40) hydrogen bonds : bond 0.04209 / 2.81 ( 446) hydrogen bonds : angle 4.82990 / 3.38 ( 1263) link_NAG-ASN : bond 0.00297 / 0.17 ( 11) link_NAG-ASN : angle 1.79462 / 1.15 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 388 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8317 (mtmt) REVERT: E 26 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.7294 (p-80) REVERT: H 13 ARG cc_start: 0.7328 (mmp80) cc_final: 0.6976 (mmm160) REVERT: H 54 ASN cc_start: 0.7575 (m110) cc_final: 0.7309 (m110) REVERT: L 55 GLU cc_start: 0.5661 (OUTLIER) cc_final: 0.5370 (pm20) outliers start: 27 outliers final: 19 residues processed: 189 average time/residue: 0.2424 time to fit residues: 69.8606 Evaluate side-chains 189 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 151 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114027 restraints weight = 62642.667| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.34 r_work: 0.3332 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 13850 Z= 0.150 Angle : 0.504 12.874 18743 Z= 0.266 Chirality : 0.040 0.211 2040 Planarity : 0.003 0.041 2451 Dihedral : 5.433 58.863 2104 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.65 % Allowed : 11.29 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.20), residues: 1689 helix: 2.40 (0.28), residues: 332 sheet: -1.88 (0.28), residues: 323 loop : -1.99 (0.17), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 98 TYR 0.013 0.001 TYR D 511 PHE 0.008 0.001 PHE D 373 TRP 0.006 0.001 TRP E 160 HIS 0.004 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (13819) covalent geometry : angle 0.48552 / 0.26 (18670) SS BOND : bond 0.00549 / 0.29 ( 20) SS BOND : angle 2.20805 / 1.32 ( 40) hydrogen bonds : bond 0.04049 / 2.70 ( 446) hydrogen bonds : angle 4.77269 / 3.34 ( 1263) link_NAG-ASN : bond 0.00320 / 0.21 ( 11) link_NAG-ASN : angle 2.28144 / 1.68 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 97 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 388 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8343 (mtmt) REVERT: E 26 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.7412 (p-80) REVERT: H 13 ARG cc_start: 0.7336 (mmp80) cc_final: 0.6975 (mmm160) REVERT: L 55 GLU cc_start: 0.5637 (OUTLIER) cc_final: 0.5356 (pm20) outliers start: 24 outliers final: 21 residues processed: 187 average time/residue: 0.2496 time to fit residues: 70.8197 Evaluate side-chains 192 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain F residue 493 CYS Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112270 restraints weight = 62804.426| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.32 r_work: 0.3303 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13850 Z= 0.239 Angle : 0.551 12.626 18743 Z= 0.293 Chirality : 0.042 0.218 2040 Planarity : 0.004 0.040 2451 Dihedral : 5.669 56.024 2104 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.79 % Allowed : 11.22 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.19), residues: 1689 helix: 2.15 (0.28), residues: 338 sheet: -1.97 (0.28), residues: 305 loop : -2.16 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.014 0.002 TYR D 468 PHE 0.015 0.001 PHE D 373 TRP 0.010 0.001 TRP E 160 HIS 0.005 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (13819) covalent geometry : angle 0.53305 / 0.29 (18670) SS BOND : bond 0.00672 / 0.34 ( 20) SS BOND : angle 2.26403 / 1.35 ( 40) hydrogen bonds : bond 0.04367 / 2.92 ( 446) hydrogen bonds : angle 4.89526 / 3.43 ( 1263) link_NAG-ASN : bond 0.00390 / 0.24 ( 11) link_NAG-ASN : angle 2.27329 / 1.64 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6012.96 seconds wall clock time: 102 minutes 54.36 seconds (6174.36 seconds total)