Starting phenix.real_space_refine on Tue Jul 29 16:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7srs_25403/07_2025/7srs_25403_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7srs_25403/07_2025/7srs_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_25403/07_2025/7srs_25403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7srs_25403/07_2025/7srs_25403.map" model { file = "/net/cci-nas-00/data/ceres_data/7srs_25403/07_2025/7srs_25403_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7srs_25403/07_2025/7srs_25403_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 4, '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: {'TYR:plan': 1, 'GLU:plan': 2, '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: {'GLU:plan': 9, 'ASN:plan1': 5, 'ARG:plan': 4, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 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: 6.35, per 1000 atoms: 0.76 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.23 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: 2.65 Time building geometry restraints manager: 2.75 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (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 TRP 0.011 0.001 TRP H 50 HIS 0.009 0.002 HIS C 345 PHE 0.014 0.002 PHE C 277 TYR 0.020 0.001 TYR Q 52 ARG 0.008 0.001 ARG C 307 Details of bonding type rmsd link_NAG-ASN : bond 0.01593 ( 1) link_NAG-ASN : angle 8.05496 ( 3) hydrogen bonds : bond 0.16530 ( 406) hydrogen bonds : angle 5.11922 ( 1191) SS BOND : bond 0.00696 ( 4) SS BOND : angle 1.44822 ( 8) covalent geometry : bond 0.00539 ( 8567) covalent geometry : angle 0.66365 (11707) *********************** 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 : 1.015 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: 0.2356 time to fit residues: 42.6259 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 : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 ASN R 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084618 restraints weight = 16329.484| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.31 r_work: 0.3087 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1020 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= 0.124 Angle : 0.563 10.883 11718 Z= 0.293 Chirality : 0.043 0.222 1374 Planarity : 0.004 0.056 1458 Dihedral : 7.133 147.027 1238 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.92 % Allowed : 7.16 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1082 helix: 3.25 (0.33), residues: 238 sheet: 1.29 (0.26), residues: 385 loop : -1.05 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.005 0.001 HIS C 345 PHE 0.018 0.001 PHE R 331 TYR 0.012 0.001 TYR R 87 ARG 0.004 0.000 ARG C 65 Details of bonding type rmsd link_NAG-ASN : bond 0.01766 ( 1) link_NAG-ASN : angle 8.20677 ( 3) hydrogen bonds : bond 0.05357 ( 406) hydrogen bonds : angle 4.14078 ( 1191) SS BOND : bond 0.00474 ( 4) SS BOND : angle 1.01958 ( 8) covalent geometry : bond 0.00253 ( 8567) covalent geometry : angle 0.54754 (11707) *********************** 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 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7726 (mmtp) REVERT: C 223 ASN cc_start: 0.7496 (t0) cc_final: 0.6991 (t0) REVERT: L 62 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7524 (mtm-85) outliers start: 8 outliers final: 7 residues processed: 121 average time/residue: 0.2198 time to fit residues: 36.2335 Evaluate side-chains 115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 33 LEU 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 101 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.098143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.083202 restraints weight = 16669.341| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.34 r_work: 0.3049 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8572 Z= 0.147 Angle : 0.568 10.512 11718 Z= 0.297 Chirality : 0.043 0.263 1374 Planarity : 0.004 0.048 1458 Dihedral : 6.998 141.894 1238 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.85 % Allowed : 8.89 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1082 helix: 3.35 (0.34), residues: 238 sheet: 1.16 (0.26), residues: 393 loop : -1.06 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 47 HIS 0.007 0.001 HIS C 345 PHE 0.026 0.002 PHE R 331 TYR 0.012 0.001 TYR R 87 ARG 0.003 0.000 ARG H 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01656 ( 1) link_NAG-ASN : angle 7.78191 ( 3) hydrogen bonds : bond 0.05692 ( 406) hydrogen bonds : angle 4.07819 ( 1191) SS BOND : bond 0.00614 ( 4) SS BOND : angle 1.23902 ( 8) covalent geometry : bond 0.00335 ( 8567) covalent geometry : angle 0.55384 (11707) *********************** 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 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7882 (mmtt) REVERT: C 223 ASN cc_start: 0.7535 (t0) cc_final: 0.6975 (t0) REVERT: L 62 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7614 (mtm-85) outliers start: 16 outliers final: 13 residues processed: 117 average time/residue: 0.2029 time to fit residues: 32.8543 Evaluate side-chains 121 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 342 ILE 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 187 THR Chi-restraints excluded: chain C residue 359 GLU 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 8 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.097396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082434 restraints weight = 16555.620| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.34 r_work: 0.3047 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8572 Z= 0.152 Angle : 0.571 10.451 11718 Z= 0.299 Chirality : 0.043 0.245 1374 Planarity : 0.004 0.045 1458 Dihedral : 6.819 133.820 1238 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.19 % Allowed : 9.82 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1082 helix: 3.40 (0.34), residues: 238 sheet: 1.20 (0.26), residues: 390 loop : -1.11 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 47 HIS 0.008 0.001 HIS C 345 PHE 0.025 0.002 PHE R 331 TYR 0.012 0.001 TYR R 87 ARG 0.004 0.000 ARG H 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01587 ( 1) link_NAG-ASN : angle 7.76197 ( 3) hydrogen bonds : bond 0.05764 ( 406) hydrogen bonds : angle 4.05267 ( 1191) SS BOND : bond 0.00634 ( 4) SS BOND : angle 1.24673 ( 8) covalent geometry : bond 0.00351 ( 8567) covalent geometry : angle 0.55702 (11707) *********************** 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 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: C 17 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7794 (mmtt) REVERT: C 223 ASN cc_start: 0.7591 (t0) cc_final: 0.6994 (t0) REVERT: C 229 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7858 (mttt) REVERT: L 62 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7462 (mtm-85) outliers start: 19 outliers final: 16 residues processed: 125 average time/residue: 0.2055 time to fit residues: 35.5713 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 316 ILE 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 187 THR 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 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.096733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081884 restraints weight = 16390.650| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.32 r_work: 0.3024 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1292 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= 0.172 Angle : 0.586 10.289 11718 Z= 0.307 Chirality : 0.044 0.254 1374 Planarity : 0.004 0.044 1458 Dihedral : 6.758 129.395 1238 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.19 % Allowed : 11.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1082 helix: 3.40 (0.34), residues: 238 sheet: 1.12 (0.26), residues: 384 loop : -1.13 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 367 HIS 0.007 0.001 HIS C 345 PHE 0.025 0.002 PHE R 331 TYR 0.013 0.001 TYR Q 80 ARG 0.004 0.000 ARG H 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01619 ( 1) link_NAG-ASN : angle 7.63490 ( 3) hydrogen bonds : bond 0.06025 ( 406) hydrogen bonds : angle 4.07106 ( 1191) SS BOND : bond 0.00699 ( 4) SS BOND : angle 1.34697 ( 8) covalent geometry : bond 0.00404 ( 8567) covalent geometry : angle 0.57195 (11707) *********************** 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 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.306 Fit side-chains REVERT: C 17 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7869 (mmtt) REVERT: C 223 ASN cc_start: 0.7661 (t0) cc_final: 0.7336 (t0) REVERT: L 62 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7541 (mtm-85) outliers start: 19 outliers final: 18 residues processed: 123 average time/residue: 0.2482 time to fit residues: 42.7805 Evaluate side-chains 129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.095887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081097 restraints weight = 16500.444| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.30 r_work: 0.3010 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1385 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= 0.185 Angle : 0.610 10.214 11718 Z= 0.320 Chirality : 0.044 0.238 1374 Planarity : 0.004 0.044 1458 Dihedral : 6.721 124.119 1238 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.12 % Allowed : 11.43 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1082 helix: 3.36 (0.34), residues: 238 sheet: 1.12 (0.26), residues: 382 loop : -1.24 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 47 HIS 0.007 0.002 HIS C 345 PHE 0.027 0.002 PHE R 331 TYR 0.014 0.001 TYR H 107 ARG 0.004 0.000 ARG Q 98 Details of bonding type rmsd link_NAG-ASN : bond 0.01519 ( 1) link_NAG-ASN : angle 7.76057 ( 3) hydrogen bonds : bond 0.06331 ( 406) hydrogen bonds : angle 4.13947 ( 1191) SS BOND : bond 0.00735 ( 4) SS BOND : angle 1.39746 ( 8) covalent geometry : bond 0.00439 ( 8567) covalent geometry : angle 0.59624 (11707) *********************** 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 142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.939 Fit side-chains REVERT: C 17 LYS cc_start: 0.8277 (mtmt) cc_final: 0.7893 (mmtt) REVERT: C 52 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6894 (mtt-85) REVERT: L 62 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7331 (mtm-85) outliers start: 27 outliers final: 24 residues processed: 130 average time/residue: 0.2083 time to fit residues: 37.1999 Evaluate side-chains 131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 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 187 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ** 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 = 0.3353 r_free = 0.3353 target = 0.095258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080403 restraints weight = 16535.825| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.31 r_work: 0.3000 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8572 Z= 0.198 Angle : 0.627 10.405 11718 Z= 0.328 Chirality : 0.044 0.263 1374 Planarity : 0.004 0.044 1458 Dihedral : 6.685 120.526 1238 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.12 % Allowed : 11.78 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1082 helix: 3.31 (0.34), residues: 238 sheet: 1.03 (0.26), residues: 390 loop : -1.28 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 47 HIS 0.007 0.002 HIS C 345 PHE 0.026 0.002 PHE R 331 TYR 0.015 0.002 TYR H 107 ARG 0.004 0.000 ARG H 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01665 ( 1) link_NAG-ASN : angle 7.74439 ( 3) hydrogen bonds : bond 0.06512 ( 406) hydrogen bonds : angle 4.16922 ( 1191) SS BOND : bond 0.00775 ( 4) SS BOND : angle 1.45475 ( 8) covalent geometry : bond 0.00474 ( 8567) covalent geometry : angle 0.61381 (11707) *********************** 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 138 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.879 Fit side-chains REVERT: C 17 LYS cc_start: 0.8289 (mtmt) cc_final: 0.7916 (mmtt) REVERT: C 52 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6883 (mtt-85) outliers start: 27 outliers final: 25 residues processed: 128 average time/residue: 0.2022 time to fit residues: 35.8355 Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 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 187 THR 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 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 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 93 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 ASN R 355 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 = 0.3292 r_free = 0.3292 target = 0.091758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.077194 restraints weight = 16856.463| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.30 r_work: 0.2946 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 8572 Z= 0.330 Angle : 0.764 9.555 11718 Z= 0.403 Chirality : 0.049 0.242 1374 Planarity : 0.005 0.045 1458 Dihedral : 7.269 128.819 1238 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.12 % Allowed : 11.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1082 helix: 2.84 (0.33), residues: 238 sheet: 0.86 (0.26), residues: 390 loop : -1.65 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 47 HIS 0.009 0.002 HIS C 345 PHE 0.030 0.003 PHE R 331 TYR 0.022 0.002 TYR H 107 ARG 0.007 0.001 ARG Q 98 Details of bonding type rmsd link_NAG-ASN : bond 0.01752 ( 1) link_NAG-ASN : angle 7.89957 ( 3) hydrogen bonds : bond 0.08332 ( 406) hydrogen bonds : angle 4.55184 ( 1191) SS BOND : bond 0.01106 ( 4) SS BOND : angle 2.07165 ( 8) covalent geometry : bond 0.00809 ( 8567) covalent geometry : angle 0.75229 (11707) *********************** 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: 27 poor density : 115 time to evaluate : 0.889 Fit side-chains REVERT: C 17 LYS cc_start: 0.8359 (mtmt) cc_final: 0.7982 (mmtp) REVERT: C 44 ASP cc_start: 0.7461 (t0) cc_final: 0.7169 (t0) REVERT: C 52 ARG cc_start: 0.7340 (mtt180) cc_final: 0.6976 (mtt-85) REVERT: H 20 SER cc_start: 0.8551 (p) cc_final: 0.8115 (t) REVERT: L 62 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7591 (mtp180) outliers start: 27 outliers final: 24 residues processed: 133 average time/residue: 0.1958 time to fit residues: 35.9072 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 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 332 LEU 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 187 THR 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 86 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 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 71 optimal weight: 0.9980 chunk 84 optimal weight: 0.0670 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.096153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081581 restraints weight = 16639.547| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.29 r_work: 0.3025 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1636 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= 0.136 Angle : 0.589 10.306 11718 Z= 0.305 Chirality : 0.043 0.231 1374 Planarity : 0.004 0.047 1458 Dihedral : 6.596 117.445 1238 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % Rotamer: Outliers : 2.42 % Allowed : 13.05 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1082 helix: 3.27 (0.34), residues: 238 sheet: 1.01 (0.26), residues: 391 loop : -1.49 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 144 HIS 0.006 0.001 HIS C 345 PHE 0.024 0.001 PHE R 331 TYR 0.010 0.001 TYR R 87 ARG 0.004 0.000 ARG H 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01557 ( 1) link_NAG-ASN : angle 7.88203 ( 3) hydrogen bonds : bond 0.05642 ( 406) hydrogen bonds : angle 4.10029 ( 1191) SS BOND : bond 0.00535 ( 4) SS BOND : angle 0.96900 ( 8) covalent geometry : bond 0.00298 ( 8567) covalent geometry : angle 0.57472 (11707) *********************** 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 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.884 Fit side-chains REVERT: C 17 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7904 (mmtt) REVERT: C 52 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6908 (mtt-85) REVERT: L 62 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7564 (mtp180) outliers start: 21 outliers final: 18 residues processed: 127 average time/residue: 0.2067 time to fit residues: 36.2013 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 R residue 64 VAL Chi-restraints excluded: chain R residue 203 ASN 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 187 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 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 4 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.0180 ------------------------------------------------------------------------------- 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 C 248 GLN ** 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 = 0.3349 r_free = 0.3349 target = 0.095094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080575 restraints weight = 16521.427| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.28 r_work: 0.3012 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8572 Z= 0.179 Angle : 0.638 10.959 11718 Z= 0.333 Chirality : 0.044 0.200 1374 Planarity : 0.004 0.047 1458 Dihedral : 6.453 109.821 1238 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.42 % Allowed : 13.74 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1082 helix: 3.24 (0.34), residues: 238 sheet: 0.98 (0.26), residues: 389 loop : -1.47 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 367 HIS 0.006 0.001 HIS C 345 PHE 0.026 0.002 PHE R 331 TYR 0.019 0.001 TYR Q 80 ARG 0.005 0.000 ARG H 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01341 ( 1) link_NAG-ASN : angle 7.69683 ( 3) hydrogen bonds : bond 0.06171 ( 406) hydrogen bonds : angle 4.13102 ( 1191) SS BOND : bond 0.00686 ( 4) SS BOND : angle 1.31797 ( 8) covalent geometry : bond 0.00421 ( 8567) covalent geometry : angle 0.62495 (11707) ********************** 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 130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.874 Fit side-chains REVERT: C 17 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7829 (mptt) REVERT: C 52 ARG cc_start: 0.7230 (mtt180) cc_final: 0.6898 (mtt-85) REVERT: C 329 VAL cc_start: 0.8431 (t) cc_final: 0.8223 (p) REVERT: L 62 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7578 (mtp180) outliers start: 21 outliers final: 19 residues processed: 124 average time/residue: 0.1972 time to fit residues: 33.9036 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 187 THR Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 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 32 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 ASN R 355 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 = 0.3375 r_free = 0.3375 target = 0.096563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081954 restraints weight = 16652.616| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.31 r_work: 0.3029 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8572 Z= 0.142 Angle : 0.600 10.586 11718 Z= 0.311 Chirality : 0.043 0.246 1374 Planarity : 0.004 0.046 1458 Dihedral : 5.832 83.611 1238 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 2.19 % Allowed : 13.97 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1082 helix: 3.33 (0.34), residues: 238 sheet: 1.07 (0.26), residues: 394 loop : -1.48 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 367 HIS 0.005 0.001 HIS R 242 PHE 0.025 0.001 PHE R 331 TYR 0.010 0.001 TYR R 87 ARG 0.005 0.000 ARG H 103 Details of bonding type rmsd link_NAG-ASN : bond 0.01578 ( 1) link_NAG-ASN : angle 7.86937 ( 3) hydrogen bonds : bond 0.05452 ( 406) hydrogen bonds : angle 3.99569 ( 1191) SS BOND : bond 0.00565 ( 4) SS BOND : angle 1.07477 ( 8) covalent geometry : bond 0.00323 ( 8567) covalent geometry : angle 0.58629 (11707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4693.66 seconds wall clock time: 82 minutes 18.30 seconds (4938.30 seconds total)