Starting phenix.real_space_refine on Thu Jul 2 21:58:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x2c_32964/07_2026/7x2c_32964.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2c_32964/07_2026/7x2c_32964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2026/7x2c_32964.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2026/7x2c_32964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2026/7x2c_32964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2026/7x2c_32964.map" model { file = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2026/7x2c_32964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2c_32964/07_2026/7x2c_32964.cif" } resolution = 3.2 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= -0.005 sd= 0.086 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 2939 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 S 56 5.16 5 Cl 2 4.86 5 C 5071 2.51 5 N 1341 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7953 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 279, 2156 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 279, 2156 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 2197 Chain: "A" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1824 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 2538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2526 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 Conformer: "B" Number of residues, atoms: 339, 2526 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 bond proxies already assigned to first conformer: 2559 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 953 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'CLR': 1, 'G3C': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS B 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 233 " occ=0.50 residue: pdb=" N ACYS B 271 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 271 " occ=0.50 Time building chain proxies: 2.25, per 1000 atoms: 0.28 Number of scatterers: 7953 At special positions: 0 Unit cell: (77.177, 101.091, 123.918, 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) Cl 2 17.00 S 56 16.00 O 1483 8.00 N 1341 7.00 C 5071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 339.9 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 44.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 removed outlier: 3.522A pdb=" N VAL F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 removed outlier: 3.620A pdb=" N LYS F 57 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 88 removed outlier: 3.815A pdb=" N PHE F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.444A pdb=" N ILE F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 136 through 161 removed outlier: 3.527A pdb=" N SER F 155 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 203 through 241 Processing helix chain 'F' and resid 265 through 298 removed outlier: 3.883A pdb=" N PHE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 309 through 332 removed outlier: 3.637A pdb=" N PHE F 313 " --> pdb=" O ASP F 309 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 334 through 344 removed outlier: 3.580A pdb=" N LYS F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.675A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.879A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.556A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.862A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.636A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.559A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.635A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.552A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.595A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.159A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.241A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.394A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.821A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.028A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.595A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.526A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.983A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.055A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1232 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: 0.92 Time building geometry restraints manager: 0.93 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: 2575 1.34 - 1.46: 2028 1.46 - 1.58: 3444 1.58 - 1.70: 6 1.70 - 1.82: 77 Bond restraints: 8130 Sorted by residual: bond pdb=" C06 G3C F 503 " pdb=" C07 G3C F 503 " ideal model delta sigma weight residual 1.523 1.650 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C07 G3C F 502 " pdb=" C08 G3C F 502 " ideal model delta sigma weight residual 1.510 1.637 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C07 G3C F 503 " pdb=" C08 G3C F 503 " ideal model delta sigma weight residual 1.510 1.632 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C06 G3C F 502 " pdb=" C07 G3C F 502 " ideal model delta sigma weight residual 1.523 1.639 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C13 CLR F 501 " pdb=" C17 CLR F 501 " ideal model delta sigma weight residual 1.550 1.438 0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 8125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 10910 2.40 - 4.80: 136 4.80 - 7.20: 26 7.20 - 9.59: 6 9.59 - 11.99: 2 Bond angle restraints: 11080 Sorted by residual: angle pdb=" C23 CLR F 501 " pdb=" C24 CLR F 501 " pdb=" C25 CLR F 501 " ideal model delta sigma weight residual 115.14 103.15 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta sigma weight residual 122.61 128.39 -5.78 1.56e+00 4.11e-01 1.37e+01 angle pdb=" N GLY B 319 " pdb=" CA GLY B 319 " pdb=" C GLY B 319 " ideal model delta sigma weight residual 110.87 116.55 -5.68 1.54e+00 4.22e-01 1.36e+01 angle pdb=" C TYR F 204 " pdb=" N ILE F 205 " pdb=" CA ILE F 205 " ideal model delta sigma weight residual 122.13 116.03 6.10 1.85e+00 2.92e-01 1.09e+01 angle pdb=" C17 CLR F 501 " pdb=" C20 CLR F 501 " pdb=" C22 CLR F 501 " ideal model delta sigma weight residual 109.45 99.78 9.67 3.00e+00 1.11e-01 1.04e+01 ... (remaining 11075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4327 17.95 - 35.90: 346 35.90 - 53.85: 62 53.85 - 71.80: 13 71.80 - 89.75: 3 Dihedral angle restraints: 4751 sinusoidal: 1734 harmonic: 3017 Sorted by residual: dihedral pdb=" CB CYS F 96 " pdb=" SG CYS F 96 " pdb=" SG CYS F 186 " pdb=" CB CYS F 186 " ideal model delta sinusoidal sigma weight residual 93.00 139.20 -46.20 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CA ILE F 201 " pdb=" C ILE F 201 " pdb=" N SER F 202 " pdb=" CA SER F 202 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA MET F 135 " pdb=" C MET F 135 " pdb=" N THR F 136 " pdb=" CA THR F 136 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1271 0.135 - 0.270: 2 0.270 - 0.405: 2 0.405 - 0.540: 0 0.540 - 0.675: 2 Chirality restraints: 1277 Sorted by residual: chirality pdb=" C13 CLR F 501 " pdb=" C12 CLR F 501 " pdb=" C14 CLR F 501 " pdb=" C17 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.93 -2.26 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C10 CLR F 501 " pdb=" C1 CLR F 501 " pdb=" C5 CLR F 501 " pdb=" C9 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.85 -2.23 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" C07 G3C F 502 " pdb=" C06 G3C F 502 " pdb=" C08 G3C F 502 " pdb=" C15 G3C F 502 " both_signs ideal model delta sigma weight residual False -2.44 -2.75 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1274 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 205 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.92e+00 pdb=" N PRO F 206 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 206 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 206 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 201 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C ILE F 201 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE F 201 " -0.019 2.00e-02 2.50e+03 pdb=" N SER F 202 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 327 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO F 328 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 328 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 328 " 0.040 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 122 2.66 - 3.22: 7579 3.22 - 3.78: 12542 3.78 - 4.34: 16750 4.34 - 4.90: 28139 Nonbonded interactions: 65132 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.102 3.040 nonbonded pdb=" OD1 ASP A 229 " pdb=" OG1 THR E 111 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" N GLY B 324 " model vdw 2.222 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 3.040 nonbonded pdb=" OG SER F 198 " pdb=" O01 G3C F 503 " model vdw 2.255 3.040 ... (remaining 65127 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=0.50 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.006 0.127 8133 Z= 0.293 Angle : 0.706 11.992 11086 Z= 0.358 Chirality : 0.051 0.675 1277 Planarity : 0.005 0.079 1403 Dihedral : 13.599 89.746 2784 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.48 % Allowed : 0.24 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1020 helix: 1.81 (0.26), residues: 406 sheet: 0.52 (0.33), residues: 224 loop : -0.48 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 227 TYR 0.021 0.001 TYR B 59 PHE 0.020 0.001 PHE A 212 TRP 0.038 0.002 TRP B 63 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.29 ( 8130) covalent geometry : angle 0.70545 / 0.36 (11080) SS BOND : bond 0.00122 / 0.06 ( 3) SS BOND : angle 1.13817 / 0.67 ( 6) hydrogen bonds : bond 0.15181 / 10.43 ( 427) hydrogen bonds : angle 6.37957 / 4.54 ( 1232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 29 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7120 (tm-30) REVERT: A 386 MET cc_start: 0.7988 (ttm) cc_final: 0.7455 (tpp) REVERT: B 137 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7337 (mmm160) REVERT: B 148 CYS cc_start: 0.8391 (t) cc_final: 0.8171 (t) REVERT: B 217 MET cc_start: 0.6838 (tmm) cc_final: 0.6290 (tmm) REVERT: D 41 CYS cc_start: 0.7902 (m) cc_final: 0.7668 (m) REVERT: D 47 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6891 (mp0) REVERT: E 82 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.0682 time to fit residues: 15.1090 Evaluate side-chains 139 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 50.0000 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 GLN ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 237 ASN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110432 restraints weight = 19483.186| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.41 r_work: 0.3264 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 8133 Z= 0.313 Angle : 0.706 6.782 11086 Z= 0.385 Chirality : 0.049 0.168 1277 Planarity : 0.005 0.083 1403 Dihedral : 4.836 23.504 1117 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.69 % Allowed : 9.67 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1020 helix: 1.61 (0.25), residues: 405 sheet: 0.32 (0.35), residues: 203 loop : -0.47 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 62 TYR 0.035 0.002 TYR B 59 PHE 0.017 0.003 PHE A 219 TRP 0.054 0.003 TRP B 63 HIS 0.008 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.31 ( 8130) covalent geometry : angle 0.70496 / 0.38 (11080) SS BOND : bond 0.00276 / 0.13 ( 3) SS BOND : angle 2.08756 / 1.17 ( 6) hydrogen bonds : bond 0.05114 / 3.51 ( 427) hydrogen bonds : angle 5.12805 / 3.65 ( 1232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7835 (tpt-90) REVERT: A 294 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7874 (mm-40) REVERT: B 217 MET cc_start: 0.6578 (tmm) cc_final: 0.6104 (tmm) REVERT: B 220 GLN cc_start: 0.7790 (tt0) cc_final: 0.7540 (tt0) REVERT: B 254 ASP cc_start: 0.7933 (t70) cc_final: 0.7682 (t70) REVERT: B 259 GLN cc_start: 0.6449 (mt0) cc_final: 0.6212 (mm-40) REVERT: D 41 CYS cc_start: 0.8191 (m) cc_final: 0.7989 (m) REVERT: D 47 GLU cc_start: 0.7753 (mt-10) cc_final: 0.6934 (mp0) outliers start: 10 outliers final: 7 residues processed: 149 average time/residue: 0.0736 time to fit residues: 15.2560 Evaluate side-chains 139 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN A 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.166885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115534 restraints weight = 24226.176| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 4.97 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8133 Z= 0.135 Angle : 0.540 5.968 11086 Z= 0.290 Chirality : 0.042 0.168 1277 Planarity : 0.004 0.070 1403 Dihedral : 4.401 22.311 1117 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.93 % Allowed : 12.58 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.26), residues: 1020 helix: 2.15 (0.25), residues: 406 sheet: 0.38 (0.35), residues: 192 loop : -0.37 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 226 TYR 0.008 0.001 TYR F 131 PHE 0.020 0.001 PHE F 288 TRP 0.033 0.002 TRP B 63 HIS 0.007 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 8130) covalent geometry : angle 0.53935 / 0.29 (11080) SS BOND : bond 0.00128 / 0.07 ( 3) SS BOND : angle 1.26271 / 0.71 ( 6) hydrogen bonds : bond 0.04193 / 2.88 ( 427) hydrogen bonds : angle 4.62299 / 3.28 ( 1232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7577 (tp40) cc_final: 0.7328 (tp40) REVERT: A 294 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7706 (mm-40) REVERT: A 317 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8395 (ttp80) REVERT: A 331 ASP cc_start: 0.7967 (t0) cc_final: 0.7719 (t0) REVERT: A 368 ASP cc_start: 0.7251 (m-30) cc_final: 0.6914 (m-30) REVERT: B 137 ARG cc_start: 0.7776 (mmm160) cc_final: 0.7311 (mmm160) REVERT: B 217 MET cc_start: 0.6137 (tmm) cc_final: 0.5723 (tmm) REVERT: B 220 GLN cc_start: 0.7777 (tt0) cc_final: 0.7541 (tt0) REVERT: B 254 ASP cc_start: 0.7793 (t70) cc_final: 0.7502 (t70) REVERT: B 298 ASP cc_start: 0.7475 (t70) cc_final: 0.6644 (t0) REVERT: D 41 CYS cc_start: 0.8168 (m) cc_final: 0.7940 (m) REVERT: D 47 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6874 (mp0) REVERT: E 49 SER cc_start: 0.8690 (m) cc_final: 0.8278 (t) outliers start: 12 outliers final: 9 residues processed: 157 average time/residue: 0.0670 time to fit residues: 14.6199 Evaluate side-chains 151 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115072 restraints weight = 26073.593| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 5.53 r_work: 0.3260 rms_B_bonded: 5.30 restraints_weight: 2.0000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8133 Z= 0.188 Angle : 0.583 7.199 11086 Z= 0.310 Chirality : 0.044 0.240 1277 Planarity : 0.004 0.069 1403 Dihedral : 4.469 23.150 1117 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.54 % Allowed : 14.15 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1020 helix: 2.08 (0.25), residues: 406 sheet: 0.35 (0.36), residues: 192 loop : -0.33 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 280 TYR 0.009 0.001 TYR F 131 PHE 0.014 0.002 PHE F 289 TRP 0.039 0.002 TRP B 63 HIS 0.006 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 8130) covalent geometry : angle 0.58216 / 0.31 (11080) SS BOND : bond 0.00168 / 0.09 ( 3) SS BOND : angle 1.36444 / 0.76 ( 6) hydrogen bonds : bond 0.04291 / 2.94 ( 427) hydrogen bonds : angle 4.60847 / 3.26 ( 1232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7639 (ttm170) cc_final: 0.7373 (mtm-85) REVERT: A 29 GLN cc_start: 0.7701 (tp40) cc_final: 0.7372 (tp40) REVERT: A 294 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7665 (mm-40) REVERT: A 317 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8449 (ttp80) REVERT: A 331 ASP cc_start: 0.7873 (t0) cc_final: 0.7621 (t0) REVERT: A 368 ASP cc_start: 0.7040 (m-30) cc_final: 0.6756 (m-30) REVERT: B 137 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7341 (mmm160) REVERT: B 198 LEU cc_start: 0.7052 (mt) cc_final: 0.6658 (mt) REVERT: B 217 MET cc_start: 0.6142 (tmm) cc_final: 0.5693 (tmm) REVERT: B 254 ASP cc_start: 0.7853 (t70) cc_final: 0.7579 (t70) REVERT: B 298 ASP cc_start: 0.7907 (t70) cc_final: 0.7073 (t0) REVERT: B 325 MET cc_start: 0.8539 (mmm) cc_final: 0.8313 (mmm) REVERT: D 41 CYS cc_start: 0.8164 (m) cc_final: 0.7941 (m) REVERT: D 47 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6921 (mp0) REVERT: E 49 SER cc_start: 0.8715 (m) cc_final: 0.8318 (t) outliers start: 17 outliers final: 13 residues processed: 162 average time/residue: 0.0700 time to fit residues: 15.8719 Evaluate side-chains 155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain E residue 31 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.168541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118509 restraints weight = 27576.769| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 5.68 r_work: 0.3301 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8133 Z= 0.118 Angle : 0.525 6.272 11086 Z= 0.280 Chirality : 0.041 0.177 1277 Planarity : 0.004 0.061 1403 Dihedral : 4.291 23.226 1117 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.81 % Allowed : 15.48 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1020 helix: 2.32 (0.25), residues: 406 sheet: 0.36 (0.36), residues: 192 loop : -0.27 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 280 TYR 0.008 0.001 TYR F 131 PHE 0.016 0.001 PHE F 288 TRP 0.021 0.002 TRP B 63 HIS 0.006 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 8130) covalent geometry : angle 0.52408 / 0.28 (11080) SS BOND : bond 0.00267 / 0.13 ( 3) SS BOND : angle 1.15664 / 0.66 ( 6) hydrogen bonds : bond 0.03871 / 2.66 ( 427) hydrogen bonds : angle 4.40367 / 3.11 ( 1232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7665 (ttm170) cc_final: 0.7406 (mtm-85) REVERT: A 280 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7529 (tpt-90) REVERT: A 294 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7613 (mm-40) REVERT: A 331 ASP cc_start: 0.7834 (t0) cc_final: 0.7538 (t0) REVERT: A 368 ASP cc_start: 0.7075 (m-30) cc_final: 0.6733 (m-30) REVERT: B 68 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7736 (mtp-110) REVERT: B 101 MET cc_start: 0.8827 (mtt) cc_final: 0.8588 (mtp) REVERT: B 137 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7330 (mmm160) REVERT: B 171 ILE cc_start: 0.7887 (mp) cc_final: 0.7436 (mp) REVERT: B 217 MET cc_start: 0.6128 (tmm) cc_final: 0.5694 (tmm) REVERT: B 220 GLN cc_start: 0.7697 (tt0) cc_final: 0.7464 (tt0) REVERT: B 254 ASP cc_start: 0.7832 (t70) cc_final: 0.7548 (t70) REVERT: B 298 ASP cc_start: 0.7891 (t70) cc_final: 0.7161 (t0) REVERT: D 41 CYS cc_start: 0.8153 (m) cc_final: 0.7892 (m) REVERT: D 47 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6977 (mp0) REVERT: E 29 PHE cc_start: 0.8365 (t80) cc_final: 0.8068 (t80) REVERT: E 49 SER cc_start: 0.8505 (m) cc_final: 0.8073 (t) outliers start: 11 outliers final: 9 residues processed: 160 average time/residue: 0.0867 time to fit residues: 18.3836 Evaluate side-chains 148 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.0270 chunk 2 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 49 optimal weight: 50.0000 chunk 96 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.169036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116349 restraints weight = 31864.226| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 5.75 r_work: 0.3286 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8133 Z= 0.144 Angle : 0.545 5.834 11086 Z= 0.291 Chirality : 0.042 0.166 1277 Planarity : 0.004 0.061 1403 Dihedral : 4.290 22.858 1117 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.26 % Allowed : 15.36 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.26), residues: 1020 helix: 2.31 (0.25), residues: 406 sheet: 0.14 (0.36), residues: 195 loop : -0.26 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.008 0.001 TYR F 131 PHE 0.015 0.001 PHE F 289 TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8130) covalent geometry : angle 0.54415 / 0.29 (11080) SS BOND : bond 0.00182 / 0.09 ( 3) SS BOND : angle 1.23351 / 0.67 ( 6) hydrogen bonds : bond 0.03968 / 2.72 ( 427) hydrogen bonds : angle 4.38774 / 3.09 ( 1232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7677 (ttm170) cc_final: 0.7398 (mtm-85) REVERT: A 294 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7628 (mm-40) REVERT: A 331 ASP cc_start: 0.7850 (t0) cc_final: 0.7530 (t0) REVERT: A 368 ASP cc_start: 0.7038 (m-30) cc_final: 0.6711 (m-30) REVERT: B 68 ARG cc_start: 0.8424 (mtp180) cc_final: 0.7873 (mtp-110) REVERT: B 101 MET cc_start: 0.8868 (mtt) cc_final: 0.8638 (mtp) REVERT: B 137 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7347 (mmm160) REVERT: B 171 ILE cc_start: 0.7914 (mp) cc_final: 0.7459 (mp) REVERT: B 217 MET cc_start: 0.6275 (tmm) cc_final: 0.5808 (tmm) REVERT: B 254 ASP cc_start: 0.7806 (t70) cc_final: 0.7521 (t70) REVERT: B 298 ASP cc_start: 0.8024 (t70) cc_final: 0.7126 (t0) REVERT: D 41 CYS cc_start: 0.8120 (m) cc_final: 0.7864 (m) REVERT: D 47 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6937 (mp0) outliers start: 23 outliers final: 14 residues processed: 158 average time/residue: 0.0731 time to fit residues: 15.9452 Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain E residue 31 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 89 optimal weight: 0.0050 chunk 65 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116148 restraints weight = 31543.580| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 5.75 r_work: 0.3284 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8133 Z= 0.144 Angle : 0.545 5.807 11086 Z= 0.291 Chirality : 0.042 0.168 1277 Planarity : 0.004 0.059 1403 Dihedral : 4.315 28.087 1117 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.02 % Allowed : 15.84 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1020 helix: 2.33 (0.25), residues: 406 sheet: 0.13 (0.36), residues: 195 loop : -0.25 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.009 0.001 TYR B 85 PHE 0.014 0.001 PHE F 289 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8130) covalent geometry : angle 0.54437 / 0.29 (11080) SS BOND : bond 0.00130 / 0.07 ( 3) SS BOND : angle 1.16625 / 0.65 ( 6) hydrogen bonds : bond 0.03935 / 2.70 ( 427) hydrogen bonds : angle 4.36609 / 3.07 ( 1232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7401 (mtm-85) REVERT: A 331 ASP cc_start: 0.7811 (t0) cc_final: 0.7491 (t0) REVERT: A 368 ASP cc_start: 0.7020 (m-30) cc_final: 0.6692 (m-30) REVERT: B 68 ARG cc_start: 0.8378 (mtp180) cc_final: 0.8052 (mtp-110) REVERT: B 101 MET cc_start: 0.8902 (mtt) cc_final: 0.8675 (mtp) REVERT: B 137 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7358 (mmm160) REVERT: B 171 ILE cc_start: 0.7954 (mp) cc_final: 0.7506 (mp) REVERT: B 217 MET cc_start: 0.6435 (tmm) cc_final: 0.5976 (tmm) REVERT: B 220 GLN cc_start: 0.7688 (tt0) cc_final: 0.7310 (tt0) REVERT: B 254 ASP cc_start: 0.7841 (t70) cc_final: 0.7545 (t70) REVERT: B 298 ASP cc_start: 0.8043 (t70) cc_final: 0.7123 (t0) REVERT: D 41 CYS cc_start: 0.8120 (m) cc_final: 0.7861 (m) REVERT: D 47 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6953 (mp0) REVERT: E 31 ASN cc_start: 0.8448 (t0) cc_final: 0.8233 (t0) outliers start: 21 outliers final: 19 residues processed: 156 average time/residue: 0.0732 time to fit residues: 15.7079 Evaluate side-chains 164 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 70 optimal weight: 0.0370 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122369 restraints weight = 28140.481| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 5.82 r_work: 0.3363 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8133 Z= 0.104 Angle : 0.525 8.510 11086 Z= 0.276 Chirality : 0.041 0.165 1277 Planarity : 0.004 0.055 1403 Dihedral : 4.192 36.552 1117 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.30 % Allowed : 16.69 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.27), residues: 1020 helix: 2.48 (0.25), residues: 407 sheet: 0.18 (0.36), residues: 196 loop : -0.21 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.009 0.001 TYR E 60 PHE 0.013 0.001 PHE F 288 TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 8130) covalent geometry : angle 0.52458 / 0.28 (11080) SS BOND : bond 0.00087 / 0.05 ( 3) SS BOND : angle 0.88360 / 0.49 ( 6) hydrogen bonds : bond 0.03556 / 2.47 ( 427) hydrogen bonds : angle 4.20819 / 2.96 ( 1232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7917 (mm-40) REVERT: A 331 ASP cc_start: 0.7791 (t0) cc_final: 0.7455 (t0) REVERT: A 368 ASP cc_start: 0.7130 (m-30) cc_final: 0.6776 (m-30) REVERT: A 386 MET cc_start: 0.8493 (ttm) cc_final: 0.7767 (tpp) REVERT: B 59 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 137 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7358 (mmm160) REVERT: B 148 CYS cc_start: 0.7961 (t) cc_final: 0.7340 (m) REVERT: B 171 ILE cc_start: 0.7913 (mp) cc_final: 0.7460 (mp) REVERT: B 217 MET cc_start: 0.6205 (tmm) cc_final: 0.5773 (tmm) REVERT: B 220 GLN cc_start: 0.7684 (tt0) cc_final: 0.7353 (tt0) REVERT: B 254 ASP cc_start: 0.7818 (t70) cc_final: 0.7546 (t70) REVERT: B 298 ASP cc_start: 0.7979 (t70) cc_final: 0.7041 (t0) REVERT: D 41 CYS cc_start: 0.8090 (m) cc_final: 0.7845 (m) REVERT: D 47 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6706 (mp0) REVERT: E 49 SER cc_start: 0.8391 (m) cc_final: 0.7982 (t) outliers start: 15 outliers final: 13 residues processed: 157 average time/residue: 0.0792 time to fit residues: 17.0862 Evaluate side-chains 158 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN B 230 ASN ** B 340 ASN ** 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 = 0.4132 r_free = 0.4132 target = 0.175331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124592 restraints weight = 26489.398| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 6.00 r_work: 0.3343 rms_B_bonded: 5.67 restraints_weight: 2.0000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8133 Z= 0.114 Angle : 0.535 7.005 11086 Z= 0.283 Chirality : 0.041 0.158 1277 Planarity : 0.004 0.056 1403 Dihedral : 4.163 35.755 1117 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.30 % Allowed : 17.78 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 1020 helix: 2.52 (0.25), residues: 409 sheet: 0.22 (0.36), residues: 196 loop : -0.21 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.008 0.001 TYR F 131 PHE 0.013 0.001 PHE F 289 TRP 0.016 0.001 TRP A 281 HIS 0.006 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8130) covalent geometry : angle 0.53507 / 0.28 (11080) SS BOND : bond 0.00068 / 0.04 ( 3) SS BOND : angle 0.94654 / 0.54 ( 6) hydrogen bonds : bond 0.03616 / 2.50 ( 427) hydrogen bonds : angle 4.19873 / 2.97 ( 1232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7392 (ttm110) cc_final: 0.6981 (mtm-85) REVERT: A 294 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7709 (mm-40) REVERT: A 331 ASP cc_start: 0.7746 (t0) cc_final: 0.7414 (t0) REVERT: A 368 ASP cc_start: 0.6991 (m-30) cc_final: 0.6666 (m-30) REVERT: A 386 MET cc_start: 0.8440 (ttm) cc_final: 0.7698 (tpp) REVERT: B 68 ARG cc_start: 0.7795 (mtp180) cc_final: 0.7411 (mmm-85) REVERT: B 137 ARG cc_start: 0.7740 (mmm160) cc_final: 0.7315 (mmm160) REVERT: B 171 ILE cc_start: 0.7861 (mp) cc_final: 0.7416 (mp) REVERT: B 217 MET cc_start: 0.6073 (tmm) cc_final: 0.5655 (tmm) REVERT: B 220 GLN cc_start: 0.7595 (tt0) cc_final: 0.7256 (tt0) REVERT: B 254 ASP cc_start: 0.7811 (t70) cc_final: 0.7569 (t70) REVERT: B 298 ASP cc_start: 0.7916 (t70) cc_final: 0.6996 (t0) REVERT: D 41 CYS cc_start: 0.8085 (m) cc_final: 0.7829 (m) REVERT: D 47 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6660 (mp0) REVERT: E 49 SER cc_start: 0.8359 (m) cc_final: 0.7955 (t) outliers start: 15 outliers final: 12 residues processed: 151 average time/residue: 0.0754 time to fit residues: 15.8705 Evaluate side-chains 155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** B 340 ASN ** 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 = 0.4143 r_free = 0.4143 target = 0.176023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125652 restraints weight = 30037.357| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 6.23 r_work: 0.3334 rms_B_bonded: 5.90 restraints_weight: 2.0000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8133 Z= 0.113 Angle : 0.544 8.671 11086 Z= 0.284 Chirality : 0.041 0.155 1277 Planarity : 0.004 0.056 1403 Dihedral : 4.153 36.404 1117 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.18 % Allowed : 17.53 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.27), residues: 1020 helix: 2.48 (0.25), residues: 413 sheet: 0.14 (0.36), residues: 198 loop : -0.19 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.008 0.001 TYR B 124 PHE 0.013 0.001 PHE F 289 TRP 0.019 0.001 TRP B 169 HIS 0.006 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8130) covalent geometry : angle 0.54348 / 0.28 (11080) SS BOND : bond 0.00047 / 0.02 ( 3) SS BOND : angle 0.92517 / 0.53 ( 6) hydrogen bonds : bond 0.03596 / 2.48 ( 427) hydrogen bonds : angle 4.17039 / 2.95 ( 1232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7369 (ttm110) cc_final: 0.6956 (mtm-85) REVERT: A 294 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7745 (mm-40) REVERT: A 331 ASP cc_start: 0.7757 (t0) cc_final: 0.7413 (t0) REVERT: A 368 ASP cc_start: 0.6962 (m-30) cc_final: 0.6634 (m-30) REVERT: A 386 MET cc_start: 0.8415 (ttm) cc_final: 0.7682 (tpp) REVERT: B 68 ARG cc_start: 0.7724 (mtp180) cc_final: 0.7521 (mmm-85) REVERT: B 137 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7348 (mmm160) REVERT: B 171 ILE cc_start: 0.7826 (mp) cc_final: 0.7383 (mp) REVERT: B 217 MET cc_start: 0.6119 (tmm) cc_final: 0.5710 (tmm) REVERT: B 220 GLN cc_start: 0.7628 (tt0) cc_final: 0.7411 (tt0) REVERT: B 254 ASP cc_start: 0.7774 (t70) cc_final: 0.7513 (t70) REVERT: B 298 ASP cc_start: 0.7892 (t70) cc_final: 0.6987 (t0) REVERT: D 41 CYS cc_start: 0.8087 (m) cc_final: 0.7839 (m) REVERT: D 47 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6830 (mp0) REVERT: E 47 TRP cc_start: 0.7469 (t60) cc_final: 0.7081 (t60) REVERT: E 49 SER cc_start: 0.8370 (m) cc_final: 0.8135 (t) outliers start: 14 outliers final: 11 residues processed: 155 average time/residue: 0.0741 time to fit residues: 15.7437 Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 0.0040 chunk 86 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125857 restraints weight = 24915.787| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 5.78 r_work: 0.3364 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8133 Z= 0.111 Angle : 0.541 8.054 11086 Z= 0.282 Chirality : 0.041 0.143 1277 Planarity : 0.004 0.056 1403 Dihedral : 4.113 36.542 1117 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.42 % Allowed : 17.53 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.27), residues: 1020 helix: 2.53 (0.25), residues: 411 sheet: 0.14 (0.36), residues: 198 loop : -0.16 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.008 0.001 TYR B 124 PHE 0.012 0.001 PHE F 289 TRP 0.018 0.001 TRP B 169 HIS 0.007 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 8130) covalent geometry : angle 0.54080 / 0.28 (11080) SS BOND : bond 0.00052 / 0.03 ( 3) SS BOND : angle 0.92771 / 0.53 ( 6) hydrogen bonds : bond 0.03531 / 2.44 ( 427) hydrogen bonds : angle 4.14142 / 2.93 ( 1232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2026.87 seconds wall clock time: 35 minutes 16.91 seconds (2116.91 seconds total)