Starting phenix.real_space_refine on Wed Mar 4 06:19:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7srs_25403/03_2026/7srs_25403_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7srs_25403/03_2026/7srs_25403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7srs_25403/03_2026/7srs_25403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7srs_25403/03_2026/7srs_25403.map" model { file = "/net/cci-nas-00/data/ceres_data/7srs_25403/03_2026/7srs_25403_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7srs_25403/03_2026/7srs_25403_neut.cif" } resolution = 3.3 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3682 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 36 5.16 5 C 5406 2.51 5 N 1381 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8361 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 768 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 959 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2234 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2682 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 326} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 9, 'ASP:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 893 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'7LD': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.03, per 1000 atoms: 0.24 Number of scatterers: 8361 At special positions: 0 Unit cell: (99.6957, 92.0268, 175.533, 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 36 16.00 P 3 15.00 O 1535 8.00 N 1381 7.00 C 5406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 87 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 350 " - pdb=" SG CYS R 353 " 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 R 501 " - " ASN R 204 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 333.1 milliseconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 25.9% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'Q' and resid 62 through 65 Processing helix chain 'R' and resid 57 through 82 removed outlier: 3.612A pdb=" N VAL R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix removed outlier: 3.585A pdb=" N GLU R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 117 removed outlier: 3.772A pdb=" N LEU R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N MET R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) Proline residue: R 109 - end of helix Processing helix chain 'R' and resid 126 through 159 removed outlier: 4.387A pdb=" N ALA R 130 " --> pdb=" O VAL R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 167 Processing helix chain 'R' and resid 168 through 188 removed outlier: 3.540A pdb=" N ALA R 172 " --> pdb=" O SER R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 193 removed outlier: 4.414A pdb=" N ILE R 192 " --> pdb=" O ILE R 188 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS R 193 " --> pdb=" O PRO R 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 188 through 193' Processing helix chain 'R' and resid 201 through 205 removed outlier: 3.524A pdb=" N ILE R 205 " --> pdb=" O PRO R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 226 removed outlier: 6.600A pdb=" N ASP R 216 " --> pdb=" O GLU R 212 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 251 removed outlier: 3.512A pdb=" N ILE R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE R 238 " --> pdb=" O ILE R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 350 Proline residue: R 339 - end of helix Processing helix chain 'R' and resid 354 through 383 removed outlier: 3.556A pdb=" N LEU R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE R 364 " --> pdb=" O MET R 360 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP R 367 " --> pdb=" O GLU R 363 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE R 368 " --> pdb=" O ILE R 364 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY R 369 " --> pdb=" O PHE R 365 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY R 374 " --> pdb=" O TYR R 370 " (cutoff:3.500A) Proline residue: R 377 - end of helix removed outlier: 3.683A pdb=" N TYR R 380 " --> pdb=" O ASN R 376 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE R 383 " --> pdb=" O VAL R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 397 removed outlier: 3.849A pdb=" N ARG R 388 " --> pdb=" O ASN R 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 removed outlier: 4.083A pdb=" N LEU C 71 " --> pdb=" O ASP C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.279A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.623A pdb=" N VAL P 19 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 10 through 12 removed outlier: 5.798A pdb=" N GLN P 36 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU P 45 " --> pdb=" O GLN P 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.759A pdb=" N GLN P 89 " --> pdb=" O THR P 96 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR P 96 " --> pdb=" O GLN P 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.764A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TRP Q 47 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'Q' and resid 109 through 112 removed outlier: 3.568A pdb=" N SER Q 101 " --> pdb=" O ASN Q 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE R 195 " --> pdb=" O THR Q 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 458 through 459 Processing sheet with id=AA9, first strand: chain 'C' and resid 26 through 28 removed outlier: 4.238A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 62 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL C 53 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLN C 85 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 26 through 28 removed outlier: 4.238A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 127 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 183 through 188 Processing sheet with id=AB3, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.878A pdb=" N PHE C 341 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR C 321 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LEU C 343 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N VAL C 319 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 231 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU C 257 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 233 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET C 255 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 235 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.869A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.208A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.208A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB8, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.363A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.363A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1191 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: 1.31 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2602 1.34 - 1.47: 2163 1.47 - 1.59: 3738 1.59 - 1.71: 12 1.71 - 1.83: 52 Bond restraints: 8567 Sorted by residual: bond pdb=" C14 7LD R 502 " pdb=" C16 7LD R 502 " ideal model delta sigma weight residual 1.525 1.403 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C11 7LD R 502 " pdb=" C9 7LD R 502 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C10 7LD R 502 " pdb=" C14 7LD R 502 " ideal model delta sigma weight residual 1.501 1.397 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C15 7LD R 502 " pdb=" C7 7LD R 502 " ideal model delta sigma weight residual 1.491 1.396 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C3 7LD R 502 " pdb=" C7 7LD R 502 " ideal model delta sigma weight residual 1.414 1.321 0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 8562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 10983 1.23 - 2.45: 586 2.45 - 3.68: 104 3.68 - 4.90: 25 4.90 - 6.13: 9 Bond angle restraints: 11707 Sorted by residual: angle pdb=" CA GLU C 134 " pdb=" C GLU C 134 " pdb=" O GLU C 134 " ideal model delta sigma weight residual 120.90 117.55 3.35 1.03e+00 9.43e-01 1.06e+01 angle pdb=" C LYS C 138 " pdb=" CA LYS C 138 " pdb=" CB LYS C 138 " ideal model delta sigma weight residual 114.40 110.64 3.76 1.25e+00 6.40e-01 9.04e+00 angle pdb=" CA LYS R 324 " pdb=" C LYS R 324 " pdb=" O LYS R 324 " ideal model delta sigma weight residual 120.82 117.86 2.96 1.05e+00 9.07e-01 7.96e+00 angle pdb=" C GLY P 67 " pdb=" N THR P 68 " pdb=" CA THR P 68 " ideal model delta sigma weight residual 122.19 126.01 -3.82 1.41e+00 5.03e-01 7.34e+00 angle pdb=" C MET R 336 " pdb=" N TRP R 337 " pdb=" CA TRP R 337 " ideal model delta sigma weight residual 122.54 118.25 4.29 1.65e+00 3.67e-01 6.76e+00 ... (remaining 11702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.35: 4952 30.35 - 60.70: 111 60.70 - 91.05: 14 91.05 - 121.40: 0 121.40 - 151.75: 1 Dihedral angle restraints: 5078 sinusoidal: 1859 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS R 128 " pdb=" SG CYS R 128 " pdb=" SG CYS R 207 " pdb=" CB CYS R 207 " ideal model delta sinusoidal sigma weight residual -86.00 -157.82 71.82 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" C16 7LD R 502 " pdb=" C17 7LD R 502 " pdb=" N3 7LD R 502 " pdb=" C18 7LD R 502 " ideal model delta sinusoidal sigma weight residual 91.75 -116.50 -151.75 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA ARG C 307 " pdb=" C ARG C 307 " pdb=" N GLU C 308 " pdb=" CA GLU C 308 " ideal model delta harmonic sigma weight residual -180.00 -158.88 -21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 5075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1190 0.066 - 0.132: 173 0.132 - 0.198: 8 0.198 - 0.264: 0 0.264 - 0.329: 3 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C14 7LD R 502 " pdb=" C10 7LD R 502 " pdb=" C13 7LD R 502 " pdb=" C16 7LD R 502 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C11 7LD R 502 " pdb=" C15 7LD R 502 " pdb=" C9 7LD R 502 " pdb=" N2 7LD R 502 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 204 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1371 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 357 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO C 358 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 358 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 358 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 275 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO C 276 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 276 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 276 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 113 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO C 114 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 114 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 114 " 0.020 5.00e-02 4.00e+02 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1538 2.77 - 3.31: 7124 3.31 - 3.84: 12313 3.84 - 4.37: 13366 4.37 - 4.90: 25900 Nonbonded interactions: 60241 Sorted by model distance: nonbonded pdb=" OD2 ASP C 29 " pdb=" NZ LYS C 170 " model vdw 2.242 3.120 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.290 3.040 nonbonded pdb=" OG SER P 7 " pdb=" OG1 THR P 22 " model vdw 2.356 3.040 nonbonded pdb=" O GLN R 320 " pdb=" OG SER R 323 " model vdw 2.375 3.040 nonbonded pdb=" O LEU R 85 " pdb=" ND2 ASN R 90 " model vdw 2.400 3.120 ... (remaining 60236 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.080 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.005 0.122 8572 Z= 0.260 Angle : 0.677 10.618 11718 Z= 0.372 Chirality : 0.046 0.329 1374 Planarity : 0.005 0.079 1458 Dihedral : 12.937 151.751 2994 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.23 % Allowed : 0.46 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.87 (0.25), residues: 1082 helix: 2.91 (0.33), residues: 238 sheet: 0.97 (0.26), residues: 403 loop : -1.17 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 307 TYR 0.020 0.001 TYR Q 52 PHE 0.014 0.002 PHE C 277 TRP 0.011 0.001 TRP H 50 HIS 0.009 0.002 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8567) covalent geometry : angle 0.66365 (11707) SS BOND : bond 0.00696 ( 4) SS BOND : angle 1.44822 ( 8) hydrogen bonds : bond 0.16530 ( 406) hydrogen bonds : angle 5.11922 ( 1191) link_NAG-ASN : bond 0.01593 ( 1) link_NAG-ASN : angle 8.05496 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.244 Fit side-chains REVERT: P 107 ARG cc_start: 0.7167 (ptm-80) cc_final: 0.5093 (ptt180) REVERT: C 17 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7808 (mmtp) REVERT: C 31 ILE cc_start: 0.7817 (mt) cc_final: 0.7612 (mt) REVERT: C 223 ASN cc_start: 0.7268 (t0) cc_final: 0.6953 (t0) REVERT: L 62 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7683 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.1078 time to fit residues: 19.5360 Evaluate side-chains 113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082691 restraints weight = 16616.877| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.32 r_work: 0.3046 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8572 Z= 0.157 Angle : 0.601 11.066 11718 Z= 0.315 Chirality : 0.044 0.216 1374 Planarity : 0.004 0.059 1458 Dihedral : 7.348 150.545 1238 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.39 % Allowed : 7.04 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 1.07 (0.25), residues: 1082 helix: 3.16 (0.33), residues: 238 sheet: 1.17 (0.26), residues: 392 loop : -1.14 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 161 TYR 0.013 0.001 TYR R 87 PHE 0.019 0.002 PHE R 331 TRP 0.007 0.001 TRP H 50 HIS 0.008 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8567) covalent geometry : angle 0.58561 (11707) SS BOND : bond 0.00618 ( 4) SS BOND : angle 1.26957 ( 8) hydrogen bonds : bond 0.06210 ( 406) hydrogen bonds : angle 4.28830 ( 1191) link_NAG-ASN : bond 0.01653 ( 1) link_NAG-ASN : angle 8.32481 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.285 Fit side-chains REVERT: C 17 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7830 (mmtp) REVERT: C 223 ASN cc_start: 0.7455 (t0) cc_final: 0.6931 (t0) REVERT: L 62 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7542 (mtm-85) outliers start: 12 outliers final: 11 residues processed: 123 average time/residue: 0.0976 time to fit residues: 16.3235 Evaluate side-chains 119 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain R residue 56 TRP Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 ASN C 248 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.081846 restraints weight = 16412.485| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.32 r_work: 0.3031 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8572 Z= 0.173 Angle : 0.601 10.920 11718 Z= 0.316 Chirality : 0.044 0.245 1374 Planarity : 0.004 0.051 1458 Dihedral : 7.282 149.040 1238 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.19 % Allowed : 9.24 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 1.03 (0.25), residues: 1082 helix: 3.24 (0.34), residues: 238 sheet: 1.12 (0.26), residues: 392 loop : -1.22 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 98 TYR 0.013 0.001 TYR R 87 PHE 0.027 0.002 PHE R 331 TRP 0.008 0.001 TRP Q 47 HIS 0.008 0.002 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8567) covalent geometry : angle 0.58586 (11707) SS BOND : bond 0.00702 ( 4) SS BOND : angle 1.38577 ( 8) hydrogen bonds : bond 0.06303 ( 406) hydrogen bonds : angle 4.22004 ( 1191) link_NAG-ASN : bond 0.01526 ( 1) link_NAG-ASN : angle 8.25441 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7839 (mmtt) REVERT: C 223 ASN cc_start: 0.7583 (t0) cc_final: 0.6987 (t0) REVERT: L 62 ARG cc_start: 0.7826 (mtm110) cc_final: 0.7456 (mtm-85) outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.0919 time to fit residues: 14.8998 Evaluate side-chains 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 6 GLN R 203 ASN R 376 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077752 restraints weight = 16768.175| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.32 r_work: 0.2942 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 8572 Z= 0.331 Angle : 0.753 10.944 11718 Z= 0.399 Chirality : 0.049 0.195 1374 Planarity : 0.005 0.052 1458 Dihedral : 7.970 161.652 1238 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.23 % Allowed : 10.16 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.55 (0.25), residues: 1082 helix: 2.78 (0.33), residues: 238 sheet: 0.91 (0.26), residues: 391 loop : -1.55 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 98 TYR 0.022 0.002 TYR H 107 PHE 0.030 0.003 PHE R 331 TRP 0.012 0.002 TRP Q 47 HIS 0.009 0.002 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00818 ( 8567) covalent geometry : angle 0.73877 (11707) SS BOND : bond 0.01063 ( 4) SS BOND : angle 2.04670 ( 8) hydrogen bonds : bond 0.08418 ( 406) hydrogen bonds : angle 4.62613 ( 1191) link_NAG-ASN : bond 0.01254 ( 1) link_NAG-ASN : angle 8.64803 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.277 Fit side-chains REVERT: C 17 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7991 (mmtt) REVERT: C 52 ARG cc_start: 0.7295 (mtt180) cc_final: 0.7001 (mtt-85) outliers start: 28 outliers final: 25 residues processed: 137 average time/residue: 0.0948 time to fit residues: 17.8171 Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 THR Chi-restraints excluded: chain R residue 56 TRP Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 348 VAL Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 99 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081944 restraints weight = 16606.451| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.33 r_work: 0.3035 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8572 Z= 0.131 Angle : 0.576 11.762 11718 Z= 0.301 Chirality : 0.043 0.242 1374 Planarity : 0.004 0.047 1458 Dihedral : 7.481 157.612 1238 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.31 % Allowed : 12.70 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.86 (0.25), residues: 1082 helix: 3.26 (0.34), residues: 238 sheet: 0.95 (0.26), residues: 399 loop : -1.38 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 103 TYR 0.012 0.001 TYR R 87 PHE 0.024 0.001 PHE R 331 TRP 0.008 0.001 TRP R 180 HIS 0.007 0.001 HIS R 242 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8567) covalent geometry : angle 0.55882 (11707) SS BOND : bond 0.00532 ( 4) SS BOND : angle 1.02714 ( 8) hydrogen bonds : bond 0.05683 ( 406) hydrogen bonds : angle 4.10216 ( 1191) link_NAG-ASN : bond 0.01471 ( 1) link_NAG-ASN : angle 8.73283 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7894 (mmtt) REVERT: C 52 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6827 (mtt-85) REVERT: L 62 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7482 (mtm-85) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.0995 time to fit residues: 17.3322 Evaluate side-chains 123 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 THR Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 375 VAL Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 ASN R 376 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.091958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.077433 restraints weight = 16609.112| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.27 r_work: 0.2944 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 8572 Z= 0.309 Angle : 0.738 10.961 11718 Z= 0.388 Chirality : 0.048 0.192 1374 Planarity : 0.005 0.050 1458 Dihedral : 8.051 168.443 1238 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.35 % Allowed : 11.78 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.52 (0.25), residues: 1082 helix: 2.88 (0.33), residues: 238 sheet: 0.87 (0.26), residues: 394 loop : -1.64 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 98 TYR 0.019 0.002 TYR H 107 PHE 0.029 0.003 PHE R 331 TRP 0.010 0.002 TRP Q 47 HIS 0.009 0.002 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00759 ( 8567) covalent geometry : angle 0.72351 (11707) SS BOND : bond 0.01014 ( 4) SS BOND : angle 1.95368 ( 8) hydrogen bonds : bond 0.08057 ( 406) hydrogen bonds : angle 4.45709 ( 1191) link_NAG-ASN : bond 0.01279 ( 1) link_NAG-ASN : angle 8.72212 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.314 Fit side-chains REVERT: C 17 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7962 (mmtt) REVERT: C 52 ARG cc_start: 0.7358 (mtt180) cc_final: 0.6999 (mtt-85) outliers start: 29 outliers final: 27 residues processed: 128 average time/residue: 0.0932 time to fit residues: 16.4039 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 375 VAL Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.080733 restraints weight = 16739.827| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.30 r_work: 0.3006 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8572 Z= 0.149 Angle : 0.599 12.012 11718 Z= 0.311 Chirality : 0.043 0.198 1374 Planarity : 0.004 0.047 1458 Dihedral : 7.696 165.130 1238 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.66 % Allowed : 13.16 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.73 (0.26), residues: 1082 helix: 3.20 (0.34), residues: 238 sheet: 0.86 (0.26), residues: 400 loop : -1.51 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 103 TYR 0.012 0.001 TYR R 87 PHE 0.025 0.002 PHE R 331 TRP 0.007 0.001 TRP R 180 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8567) covalent geometry : angle 0.58129 (11707) SS BOND : bond 0.00593 ( 4) SS BOND : angle 1.10631 ( 8) hydrogen bonds : bond 0.06010 ( 406) hydrogen bonds : angle 4.11976 ( 1191) link_NAG-ASN : bond 0.01491 ( 1) link_NAG-ASN : angle 9.00041 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.338 Fit side-chains REVERT: C 17 LYS cc_start: 0.8387 (mtmt) cc_final: 0.7973 (mmtp) REVERT: C 52 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6981 (mtt-85) REVERT: C 329 VAL cc_start: 0.8442 (t) cc_final: 0.8241 (p) REVERT: L 62 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7621 (mtp180) outliers start: 23 outliers final: 21 residues processed: 126 average time/residue: 0.1006 time to fit residues: 17.2824 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 375 VAL Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081785 restraints weight = 16523.911| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.28 r_work: 0.3027 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8572 Z= 0.139 Angle : 0.588 11.904 11718 Z= 0.304 Chirality : 0.043 0.205 1374 Planarity : 0.004 0.050 1458 Dihedral : 7.489 162.621 1238 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.77 % Allowed : 13.51 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.89 (0.26), residues: 1082 helix: 3.41 (0.34), residues: 238 sheet: 0.92 (0.26), residues: 405 loop : -1.45 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 161 TYR 0.015 0.001 TYR Q 80 PHE 0.026 0.001 PHE R 331 TRP 0.008 0.001 TRP R 367 HIS 0.005 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8567) covalent geometry : angle 0.56989 (11707) SS BOND : bond 0.00575 ( 4) SS BOND : angle 1.09494 ( 8) hydrogen bonds : bond 0.05489 ( 406) hydrogen bonds : angle 3.96981 ( 1191) link_NAG-ASN : bond 0.01561 ( 1) link_NAG-ASN : angle 8.93008 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7907 (mmtt) REVERT: C 52 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6865 (mtt-85) REVERT: L 62 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7589 (mtp180) outliers start: 24 outliers final: 22 residues processed: 129 average time/residue: 0.0961 time to fit residues: 17.2305 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 342 ILE Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 375 VAL Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078631 restraints weight = 16609.190| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.28 r_work: 0.2967 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8572 Z= 0.242 Angle : 0.688 11.433 11718 Z= 0.358 Chirality : 0.046 0.194 1374 Planarity : 0.005 0.049 1458 Dihedral : 7.883 168.378 1238 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 2.54 % Allowed : 13.97 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.64 (0.26), residues: 1082 helix: 3.10 (0.34), residues: 238 sheet: 0.90 (0.26), residues: 396 loop : -1.62 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 103 TYR 0.016 0.002 TYR H 107 PHE 0.024 0.002 PHE R 331 TRP 0.009 0.001 TRP Q 47 HIS 0.007 0.002 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 8567) covalent geometry : angle 0.67173 (11707) SS BOND : bond 0.00866 ( 4) SS BOND : angle 1.68265 ( 8) hydrogen bonds : bond 0.07217 ( 406) hydrogen bonds : angle 4.26532 ( 1191) link_NAG-ASN : bond 0.01350 ( 1) link_NAG-ASN : angle 8.82408 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7953 (mmtt) REVERT: C 52 ARG cc_start: 0.7324 (mtt180) cc_final: 0.6969 (mtt-85) REVERT: L 62 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7570 (mtp180) outliers start: 22 outliers final: 21 residues processed: 124 average time/residue: 0.1033 time to fit residues: 17.1567 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080426 restraints weight = 16499.615| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.28 r_work: 0.3000 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8572 Z= 0.166 Angle : 0.629 11.788 11718 Z= 0.325 Chirality : 0.044 0.197 1374 Planarity : 0.004 0.048 1458 Dihedral : 7.707 166.594 1238 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.54 % Allowed : 14.09 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.75 (0.26), residues: 1082 helix: 3.23 (0.34), residues: 238 sheet: 0.90 (0.26), residues: 395 loop : -1.50 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 103 TYR 0.012 0.001 TYR R 87 PHE 0.024 0.002 PHE R 331 TRP 0.008 0.001 TRP R 367 HIS 0.006 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8567) covalent geometry : angle 0.61200 (11707) SS BOND : bond 0.00656 ( 4) SS BOND : angle 1.23138 ( 8) hydrogen bonds : bond 0.06161 ( 406) hydrogen bonds : angle 4.09895 ( 1191) link_NAG-ASN : bond 0.01497 ( 1) link_NAG-ASN : angle 8.91412 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.8407 (mtmt) cc_final: 0.7949 (mmtt) REVERT: C 52 ARG cc_start: 0.7284 (mtt180) cc_final: 0.6942 (mtt-85) REVERT: C 329 VAL cc_start: 0.8442 (t) cc_final: 0.8222 (p) REVERT: L 62 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7557 (mtp180) outliers start: 22 outliers final: 22 residues processed: 121 average time/residue: 0.0950 time to fit residues: 15.7065 Evaluate side-chains 130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 109 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.082678 restraints weight = 16546.559| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.32 r_work: 0.3042 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8572 Z= 0.126 Angle : 0.578 12.067 11718 Z= 0.294 Chirality : 0.042 0.207 1374 Planarity : 0.004 0.051 1458 Dihedral : 7.381 161.265 1238 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % Rotamer: Outliers : 2.42 % Allowed : 14.09 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.92 (0.26), residues: 1082 helix: 3.44 (0.34), residues: 238 sheet: 1.07 (0.27), residues: 395 loop : -1.50 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 103 TYR 0.009 0.001 TYR R 87 PHE 0.025 0.001 PHE R 331 TRP 0.010 0.001 TRP R 56 HIS 0.006 0.001 HIS R 242 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8567) covalent geometry : angle 0.55915 (11707) SS BOND : bond 0.00486 ( 4) SS BOND : angle 0.95449 ( 8) hydrogen bonds : bond 0.04963 ( 406) hydrogen bonds : angle 3.87220 ( 1191) link_NAG-ASN : bond 0.01581 ( 1) link_NAG-ASN : angle 8.98662 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.78 seconds wall clock time: 37 minutes 25.86 seconds (2245.86 seconds total)