Starting phenix.real_space_refine on Mon Aug 25 10:51:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhs_16068/08_2025/8bhs_16068_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhs_16068/08_2025/8bhs_16068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bhs_16068/08_2025/8bhs_16068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhs_16068/08_2025/8bhs_16068.map" model { file = "/net/cci-nas-00/data/ceres_data/8bhs_16068/08_2025/8bhs_16068_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhs_16068/08_2025/8bhs_16068_trim.cif" } resolution = 3.24 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 5 7.06 5 S 85 5.16 5 C 8900 2.51 5 N 2285 2.21 5 O 2470 1.98 5 F 10 1.80 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27170 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'QK9': 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 Restraints were copied for chains: B, C, D, E Time building chain proxies: 5.57, per 1000 atoms: 0.21 Number of scatterers: 27170 At special positions: 0 Unit cell: (93.45, 92.4, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 5 34.99 S 85 16.00 F 10 9.00 O 2470 8.00 N 2285 7.00 C 8900 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 881.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 40.2% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.539A pdb=" N THR A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.809A pdb=" N ALA A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.505A pdb=" N SER A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 254 through 280 removed outlier: 3.509A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 317 through 418 removed outlier: 3.608A pdb=" N LYS A 393 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.539A pdb=" N THR B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.809A pdb=" N ALA B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 233 through 246 removed outlier: 3.506A pdb=" N SER B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 254 through 280 removed outlier: 3.509A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 314 Processing helix chain 'B' and resid 317 through 418 removed outlier: 3.608A pdb=" N LYS B 393 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.539A pdb=" N THR C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.808A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.505A pdb=" N SER C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.508A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 317 through 418 removed outlier: 3.608A pdb=" N LYS C 393 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.539A pdb=" N THR D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.809A pdb=" N ALA D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 95' Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 233 through 246 removed outlier: 3.506A pdb=" N SER D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 254 through 280 removed outlier: 3.509A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 314 Processing helix chain 'D' and resid 317 through 418 removed outlier: 3.608A pdb=" N LYS D 393 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.539A pdb=" N THR E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.808A pdb=" N ALA E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER E 95 " --> pdb=" O ASN E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 95' Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 233 through 246 removed outlier: 3.506A pdb=" N SER E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 254 through 280 removed outlier: 3.509A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 314 Processing helix chain 'E' and resid 317 through 418 removed outlier: 3.607A pdb=" N LYS E 393 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.644A pdb=" N THR A 137 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP A 66 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 53 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.498A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 removed outlier: 4.589A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.645A pdb=" N THR B 137 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP B 66 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE B 53 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 124 removed outlier: 4.497A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 103 removed outlier: 4.589A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 110 through 112 removed outlier: 3.644A pdb=" N THR C 137 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP C 66 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE C 53 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.497A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.590A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 110 through 112 removed outlier: 3.643A pdb=" N THR D 137 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP D 66 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE D 53 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 124 removed outlier: 4.497A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 103 removed outlier: 4.589A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 110 through 112 removed outlier: 3.645A pdb=" N THR E 137 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP E 66 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE E 53 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 124 removed outlier: 4.497A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.589A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 13415 1.05 - 1.26: 2100 1.26 - 1.47: 6080 1.47 - 1.69: 5795 1.69 - 1.90: 155 Bond restraints: 27545 Sorted by residual: bond pdb=" N3 QK9 A 502 " pdb=" N4 QK9 A 502 " ideal model delta sigma weight residual 1.331 1.368 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" N3 QK9 E 502 " pdb=" N4 QK9 E 502 " ideal model delta sigma weight residual 1.331 1.368 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" N3 QK9 C 502 " pdb=" N4 QK9 C 502 " ideal model delta sigma weight residual 1.331 1.368 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" N3 QK9 D 502 " pdb=" N4 QK9 D 502 " ideal model delta sigma weight residual 1.331 1.368 -0.037 2.00e-02 2.50e+03 3.34e+00 bond pdb=" N3 QK9 B 502 " pdb=" N4 QK9 B 502 " ideal model delta sigma weight residual 1.331 1.367 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 27540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 48062 1.16 - 2.33: 1306 2.33 - 3.49: 107 3.49 - 4.66: 25 4.66 - 5.82: 15 Bond angle restraints: 49515 Sorted by residual: angle pdb=" N ILE D 15 " pdb=" CA ILE D 15 " pdb=" C ILE D 15 " ideal model delta sigma weight residual 112.96 109.03 3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" N ILE C 15 " pdb=" CA ILE C 15 " pdb=" C ILE C 15 " ideal model delta sigma weight residual 112.96 109.06 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" N ILE E 15 " pdb=" CA ILE E 15 " pdb=" C ILE E 15 " ideal model delta sigma weight residual 112.96 109.06 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" N ILE A 15 " pdb=" CA ILE A 15 " pdb=" C ILE A 15 " ideal model delta sigma weight residual 112.96 109.06 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" N ILE B 15 " pdb=" CA ILE B 15 " pdb=" C ILE B 15 " ideal model delta sigma weight residual 112.96 109.09 3.87 1.00e+00 1.00e+00 1.50e+01 ... (remaining 49510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.44: 12412 14.44 - 28.88: 461 28.88 - 43.33: 132 43.33 - 57.77: 105 57.77 - 72.21: 10 Dihedral angle restraints: 13120 sinusoidal: 6990 harmonic: 6130 Sorted by residual: dihedral pdb=" CA LEU A 93 " pdb=" CB LEU A 93 " pdb=" CG LEU A 93 " pdb=" CD1 LEU A 93 " ideal model delta sinusoidal sigma weight residual 180.00 137.02 42.98 3 1.50e+01 4.44e-03 7.72e+00 dihedral pdb=" CA LEU D 93 " pdb=" CB LEU D 93 " pdb=" CG LEU D 93 " pdb=" CD1 LEU D 93 " ideal model delta sinusoidal sigma weight residual 180.00 137.03 42.97 3 1.50e+01 4.44e-03 7.72e+00 dihedral pdb=" CA LEU C 93 " pdb=" CB LEU C 93 " pdb=" CG LEU C 93 " pdb=" CD1 LEU C 93 " ideal model delta sinusoidal sigma weight residual 180.00 137.04 42.96 3 1.50e+01 4.44e-03 7.72e+00 ... (remaining 13117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1203 0.024 - 0.048: 628 0.048 - 0.071: 164 0.071 - 0.095: 80 0.095 - 0.119: 85 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE E 65 " pdb=" N ILE E 65 " pdb=" C ILE E 65 " pdb=" CB ILE E 65 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 2157 not shown) Planarity restraints: 3995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 QK9 C 502 " -0.017 2.00e-02 2.50e+03 1.38e-02 4.28e+00 pdb=" C4 QK9 C 502 " -0.004 2.00e-02 2.50e+03 pdb=" C5 QK9 C 502 " 0.002 2.00e-02 2.50e+03 pdb=" C6 QK9 C 502 " 0.007 2.00e-02 2.50e+03 pdb=" C7 QK9 C 502 " 0.001 2.00e-02 2.50e+03 pdb=" C8 QK9 C 502 " -0.013 2.00e-02 2.50e+03 pdb=" C9 QK9 C 502 " -0.016 2.00e-02 2.50e+03 pdb=" N1 QK9 C 502 " 0.028 2.00e-02 2.50e+03 pdb="BR QK9 C 502 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 QK9 B 502 " 0.018 2.00e-02 2.50e+03 1.37e-02 4.25e+00 pdb=" C4 QK9 B 502 " 0.004 2.00e-02 2.50e+03 pdb=" C5 QK9 B 502 " -0.002 2.00e-02 2.50e+03 pdb=" C6 QK9 B 502 " -0.007 2.00e-02 2.50e+03 pdb=" C7 QK9 B 502 " -0.001 2.00e-02 2.50e+03 pdb=" C8 QK9 B 502 " 0.014 2.00e-02 2.50e+03 pdb=" C9 QK9 B 502 " 0.015 2.00e-02 2.50e+03 pdb=" N1 QK9 B 502 " -0.027 2.00e-02 2.50e+03 pdb="BR QK9 B 502 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 QK9 E 502 " 0.017 2.00e-02 2.50e+03 1.37e-02 4.24e+00 pdb=" C4 QK9 E 502 " 0.004 2.00e-02 2.50e+03 pdb=" C5 QK9 E 502 " -0.002 2.00e-02 2.50e+03 pdb=" C6 QK9 E 502 " -0.007 2.00e-02 2.50e+03 pdb=" C7 QK9 E 502 " -0.001 2.00e-02 2.50e+03 pdb=" C8 QK9 E 502 " 0.013 2.00e-02 2.50e+03 pdb=" C9 QK9 E 502 " 0.015 2.00e-02 2.50e+03 pdb=" N1 QK9 E 502 " -0.028 2.00e-02 2.50e+03 pdb="BR QK9 E 502 " -0.012 2.00e-02 2.50e+03 ... (remaining 3992 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.29: 4621 2.29 - 2.89: 64455 2.89 - 3.49: 72987 3.49 - 4.10: 107046 4.10 - 4.70: 165430 Nonbonded interactions: 414539 Sorted by model distance: nonbonded pdb=" OE1 GLU C 253 " pdb=" H GLU C 253 " model vdw 1.687 2.450 nonbonded pdb=" OE1 GLU B 253 " pdb=" H GLU B 253 " model vdw 1.688 2.450 nonbonded pdb=" OE1 GLU E 253 " pdb=" H GLU E 253 " model vdw 1.688 2.450 nonbonded pdb=" OE1 GLU D 253 " pdb=" H GLU D 253 " model vdw 1.689 2.450 nonbonded pdb=" OE1 GLU A 253 " pdb=" H GLU A 253 " model vdw 1.689 2.450 ... (remaining 414534 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.580 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14140 Z= 0.118 Angle : 0.425 5.821 19265 Z= 0.214 Chirality : 0.037 0.119 2160 Planarity : 0.003 0.025 2390 Dihedral : 7.132 72.210 5110 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 1.23 (0.22), residues: 1670 helix: 2.66 (0.23), residues: 550 sheet: -0.15 (0.25), residues: 505 loop : 0.06 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 34 TYR 0.004 0.001 TYR A 172 PHE 0.005 0.001 PHE A 104 TRP 0.003 0.000 TRP A 414 HIS 0.001 0.000 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00254 (14130) covalent geometry : angle 0.42348 (19240) SS BOND : bond 0.00064 ( 5) SS BOND : angle 0.22678 ( 10) hydrogen bonds : bond 0.26192 ( 685) hydrogen bonds : angle 7.77494 ( 1965) link_NAG-ASN : bond 0.00058 ( 5) link_NAG-ASN : angle 1.53957 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 GLN cc_start: 0.8878 (tp40) cc_final: 0.8525 (tp40) REVERT: B 289 MET cc_start: 0.8674 (ttp) cc_final: 0.8317 (ttp) REVERT: C 232 GLN cc_start: 0.8888 (tp40) cc_final: 0.8515 (tp40) REVERT: E 289 MET cc_start: 0.8733 (ttp) cc_final: 0.8509 (ttp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2482 time to fit residues: 53.0285 Evaluate side-chains 95 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 105 HIS A 106 ASN B 85 GLN B 105 HIS B 106 ASN C 85 GLN C 105 HIS C 106 ASN D 85 GLN D 105 HIS D 106 ASN E 85 GLN E 105 HIS E 106 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.078771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067098 restraints weight = 104900.238| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.91 r_work: 0.3120 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14140 Z= 0.189 Angle : 0.495 4.396 19265 Z= 0.267 Chirality : 0.040 0.141 2160 Planarity : 0.004 0.036 2390 Dihedral : 3.415 12.012 1975 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.27 % Allowed : 4.70 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 1.07 (0.21), residues: 1670 helix: 2.80 (0.21), residues: 580 sheet: -0.61 (0.24), residues: 480 loop : -0.14 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 258 TYR 0.009 0.001 TYR D 417 PHE 0.008 0.001 PHE D 229 TRP 0.005 0.001 TRP E 414 HIS 0.002 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00421 (14130) covalent geometry : angle 0.49362 (19240) SS BOND : bond 0.00528 ( 5) SS BOND : angle 0.60124 ( 10) hydrogen bonds : bond 0.05104 ( 685) hydrogen bonds : angle 5.03782 ( 1965) link_NAG-ASN : bond 0.00178 ( 5) link_NAG-ASN : angle 1.34480 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 115 MET cc_start: 0.8393 (mmt) cc_final: 0.8189 (mmt) outliers start: 4 outliers final: 4 residues processed: 101 average time/residue: 0.1844 time to fit residues: 30.6821 Evaluate side-chains 94 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 410 ASN C 410 ASN D 410 ASN E 410 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065733 restraints weight = 105584.914| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.95 r_work: 0.3001 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14140 Z= 0.155 Angle : 0.456 5.404 19265 Z= 0.238 Chirality : 0.039 0.133 2160 Planarity : 0.004 0.042 2390 Dihedral : 3.404 13.789 1975 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.81 % Allowed : 4.70 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 1.02 (0.21), residues: 1670 helix: 2.99 (0.21), residues: 575 sheet: -0.73 (0.24), residues: 480 loop : -0.31 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 320 TYR 0.010 0.001 TYR E 417 PHE 0.010 0.001 PHE E 104 TRP 0.005 0.001 TRP A 291 HIS 0.002 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00336 (14130) covalent geometry : angle 0.45428 (19240) SS BOND : bond 0.00304 ( 5) SS BOND : angle 0.37383 ( 10) hydrogen bonds : bond 0.04177 ( 685) hydrogen bonds : angle 4.52953 ( 1965) link_NAG-ASN : bond 0.00080 ( 5) link_NAG-ASN : angle 1.44421 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8749 (pm20) REVERT: E 115 MET cc_start: 0.8479 (mmt) cc_final: 0.8189 (mmt) REVERT: E 289 MET cc_start: 0.8752 (ttp) cc_final: 0.8525 (ttp) outliers start: 12 outliers final: 5 residues processed: 98 average time/residue: 0.2037 time to fit residues: 30.9211 Evaluate side-chains 93 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 114 TRP Chi-restraints excluded: chain E residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 136 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.060312 restraints weight = 94778.349| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.62 r_work: 0.2899 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14140 Z= 0.199 Angle : 0.463 4.690 19265 Z= 0.245 Chirality : 0.039 0.131 2160 Planarity : 0.004 0.041 2390 Dihedral : 3.557 13.004 1975 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.01 % Allowed : 4.30 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 0.90 (0.21), residues: 1670 helix: 3.02 (0.21), residues: 575 sheet: -0.92 (0.23), residues: 480 loop : -0.41 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.008 0.001 TYR E 132 PHE 0.013 0.001 PHE E 104 TRP 0.006 0.001 TRP E 291 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00439 (14130) covalent geometry : angle 0.46110 (19240) SS BOND : bond 0.00341 ( 5) SS BOND : angle 0.46566 ( 10) hydrogen bonds : bond 0.03770 ( 685) hydrogen bonds : angle 4.47255 ( 1965) link_NAG-ASN : bond 0.00221 ( 5) link_NAG-ASN : angle 1.59472 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 115 MET cc_start: 0.8750 (mmp) cc_final: 0.8543 (mmt) outliers start: 15 outliers final: 6 residues processed: 98 average time/residue: 0.2418 time to fit residues: 36.6777 Evaluate side-chains 92 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 317 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN C 317 GLN E 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.060665 restraints weight = 95533.539| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.65 r_work: 0.2913 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14140 Z= 0.139 Angle : 0.434 4.992 19265 Z= 0.226 Chirality : 0.038 0.128 2160 Planarity : 0.004 0.042 2390 Dihedral : 3.383 12.580 1975 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.54 % Allowed : 5.44 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 0.94 (0.21), residues: 1670 helix: 3.11 (0.21), residues: 575 sheet: -0.95 (0.23), residues: 480 loop : -0.39 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 190 TYR 0.008 0.001 TYR D 417 PHE 0.010 0.001 PHE E 104 TRP 0.004 0.001 TRP C 414 HIS 0.001 0.000 HIS E 221 Details of bonding type rmsd covalent geometry : bond 0.00305 (14130) covalent geometry : angle 0.43206 (19240) SS BOND : bond 0.00308 ( 5) SS BOND : angle 0.51977 ( 10) hydrogen bonds : bond 0.03537 ( 685) hydrogen bonds : angle 4.33768 ( 1965) link_NAG-ASN : bond 0.00101 ( 5) link_NAG-ASN : angle 1.51010 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: B 115 MET cc_start: 0.8058 (tpp) cc_final: 0.7574 (mmp) REVERT: C 245 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: E 115 MET cc_start: 0.8766 (mmp) cc_final: 0.8522 (mmt) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.1909 time to fit residues: 29.3135 Evaluate side-chains 92 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 24 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.076659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065521 restraints weight = 106726.346| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.82 r_work: 0.2984 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14140 Z= 0.140 Angle : 0.429 4.637 19265 Z= 0.223 Chirality : 0.038 0.128 2160 Planarity : 0.004 0.042 2390 Dihedral : 3.346 12.219 1975 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.67 % Allowed : 5.64 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 0.97 (0.21), residues: 1670 helix: 3.18 (0.21), residues: 575 sheet: -0.97 (0.23), residues: 480 loop : -0.38 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 320 TYR 0.008 0.001 TYR D 417 PHE 0.010 0.001 PHE E 104 TRP 0.004 0.001 TRP C 414 HIS 0.001 0.000 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00308 (14130) covalent geometry : angle 0.42666 (19240) SS BOND : bond 0.00303 ( 5) SS BOND : angle 0.53349 ( 10) hydrogen bonds : bond 0.03386 ( 685) hydrogen bonds : angle 4.25564 ( 1965) link_NAG-ASN : bond 0.00107 ( 5) link_NAG-ASN : angle 1.50145 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8537 (mp10) REVERT: B 115 MET cc_start: 0.8296 (tpp) cc_final: 0.7835 (mmp) REVERT: C 245 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: D 245 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8144 (mp10) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 0.1869 time to fit residues: 28.7159 Evaluate side-chains 97 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.060401 restraints weight = 95478.946| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.67 r_work: 0.2898 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14140 Z= 0.143 Angle : 0.426 4.658 19265 Z= 0.222 Chirality : 0.038 0.127 2160 Planarity : 0.004 0.041 2390 Dihedral : 3.353 12.374 1975 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.81 % Allowed : 5.44 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 1.00 (0.22), residues: 1670 helix: 3.16 (0.21), residues: 580 sheet: -1.00 (0.23), residues: 480 loop : -0.31 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 120 TYR 0.007 0.001 TYR D 417 PHE 0.010 0.001 PHE E 104 TRP 0.004 0.001 TRP C 414 HIS 0.001 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00316 (14130) covalent geometry : angle 0.42387 (19240) SS BOND : bond 0.00311 ( 5) SS BOND : angle 0.57974 ( 10) hydrogen bonds : bond 0.03298 ( 685) hydrogen bonds : angle 4.21608 ( 1965) link_NAG-ASN : bond 0.00118 ( 5) link_NAG-ASN : angle 1.47807 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8466 (mp10) REVERT: B 115 MET cc_start: 0.8236 (tpp) cc_final: 0.7780 (mmp) REVERT: B 245 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8242 (mp10) REVERT: C 245 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: D 245 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8177 (mp10) outliers start: 12 outliers final: 5 residues processed: 97 average time/residue: 0.1824 time to fit residues: 28.6161 Evaluate side-chains 98 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.071209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.060938 restraints weight = 95833.050| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.67 r_work: 0.2918 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14140 Z= 0.112 Angle : 0.419 4.516 19265 Z= 0.215 Chirality : 0.038 0.125 2160 Planarity : 0.004 0.041 2390 Dihedral : 3.254 12.210 1975 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.74 % Allowed : 5.37 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 1.08 (0.22), residues: 1670 helix: 3.23 (0.21), residues: 580 sheet: -0.96 (0.24), residues: 480 loop : -0.27 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 224 TYR 0.008 0.001 TYR D 417 PHE 0.008 0.001 PHE E 104 TRP 0.004 0.001 TRP A 414 HIS 0.001 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00246 (14130) covalent geometry : angle 0.41678 (19240) SS BOND : bond 0.00297 ( 5) SS BOND : angle 0.56314 ( 10) hydrogen bonds : bond 0.03157 ( 685) hydrogen bonds : angle 4.14153 ( 1965) link_NAG-ASN : bond 0.00034 ( 5) link_NAG-ASN : angle 1.40693 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: B 115 MET cc_start: 0.8156 (tpp) cc_final: 0.7709 (mmp) REVERT: B 245 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: C 245 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: D 245 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8175 (mp10) outliers start: 11 outliers final: 4 residues processed: 95 average time/residue: 0.1955 time to fit residues: 29.9550 Evaluate side-chains 97 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 114 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.060638 restraints weight = 95843.307| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.71 r_work: 0.2901 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14140 Z= 0.135 Angle : 0.427 4.421 19265 Z= 0.220 Chirality : 0.038 0.126 2160 Planarity : 0.004 0.041 2390 Dihedral : 3.301 12.307 1975 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.94 % Allowed : 5.30 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 1.04 (0.22), residues: 1670 helix: 3.23 (0.21), residues: 580 sheet: -1.00 (0.23), residues: 480 loop : -0.30 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 190 TYR 0.007 0.001 TYR D 417 PHE 0.010 0.001 PHE D 104 TRP 0.005 0.001 TRP E 114 HIS 0.001 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00296 (14130) covalent geometry : angle 0.42489 (19240) SS BOND : bond 0.00310 ( 5) SS BOND : angle 0.59374 ( 10) hydrogen bonds : bond 0.03185 ( 685) hydrogen bonds : angle 4.14403 ( 1965) link_NAG-ASN : bond 0.00100 ( 5) link_NAG-ASN : angle 1.43478 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: B 115 MET cc_start: 0.8244 (tpp) cc_final: 0.7816 (mmp) REVERT: B 245 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: C 245 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: D 245 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8184 (mp10) outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 0.1929 time to fit residues: 30.7649 Evaluate side-chains 103 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 114 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.070464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.060190 restraints weight = 96900.256| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.68 r_work: 0.2896 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14140 Z= 0.164 Angle : 0.442 4.564 19265 Z= 0.229 Chirality : 0.038 0.126 2160 Planarity : 0.004 0.042 2390 Dihedral : 3.395 12.524 1975 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.74 % Allowed : 5.44 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 0.99 (0.22), residues: 1670 helix: 3.21 (0.21), residues: 580 sheet: -1.06 (0.23), residues: 480 loop : -0.32 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 190 TYR 0.007 0.001 TYR D 417 PHE 0.011 0.001 PHE E 104 TRP 0.005 0.001 TRP E 114 HIS 0.001 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00362 (14130) covalent geometry : angle 0.44031 (19240) SS BOND : bond 0.00323 ( 5) SS BOND : angle 0.59703 ( 10) hydrogen bonds : bond 0.03267 ( 685) hydrogen bonds : angle 4.18739 ( 1965) link_NAG-ASN : bond 0.00162 ( 5) link_NAG-ASN : angle 1.49883 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8531 (mp10) REVERT: B 245 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: C 245 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: D 245 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8266 (mp10) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.1918 time to fit residues: 29.8470 Evaluate side-chains 101 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 114 TRP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 14 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.060805 restraints weight = 95380.421| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.66 r_work: 0.2905 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14140 Z= 0.127 Angle : 0.430 5.657 19265 Z= 0.220 Chirality : 0.038 0.124 2160 Planarity : 0.004 0.042 2390 Dihedral : 3.307 12.339 1975 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.81 % Allowed : 5.44 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 aren not related in a simple way. whole: 1.12 (0.21), residues: 1670 helix: 3.26 (0.21), residues: 580 sheet: -0.88 (0.24), residues: 445 loop : -0.35 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 224 TYR 0.008 0.001 TYR D 417 PHE 0.009 0.001 PHE E 104 TRP 0.004 0.001 TRP C 414 HIS 0.001 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00279 (14130) covalent geometry : angle 0.42785 (19240) SS BOND : bond 0.00307 ( 5) SS BOND : angle 0.59171 ( 10) hydrogen bonds : bond 0.03153 ( 685) hydrogen bonds : angle 4.12278 ( 1965) link_NAG-ASN : bond 0.00076 ( 5) link_NAG-ASN : angle 1.43738 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4841.63 seconds wall clock time: 83 minutes 13.26 seconds (4993.26 seconds total)