Starting phenix.real_space_refine on Wed Mar 4 08:32:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fih_31597/03_2026/7fih_31597_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fih_31597/03_2026/7fih_31597.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7fih_31597/03_2026/7fih_31597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fih_31597/03_2026/7fih_31597.map" model { file = "/net/cci-nas-00/data/ceres_data/7fih_31597/03_2026/7fih_31597_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fih_31597/03_2026/7fih_31597_neut.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= 0.002 sd= 0.040 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 1455 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: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 6885 2.51 5 N 1872 2.21 5 O 2005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10853 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1972 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4314 Classifications: {'peptide': 550} Incomplete info: {'backbone_only': 9} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 525} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "X" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 679 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "Y" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'55Z': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.21 Number of scatterers: 10853 At special positions: 0 Unit cell: (82.612, 97.83, 186.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2005 8.00 N 1872 7.00 C 6885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 156 " distance=2.05 Simple disulfide: pdb=" SG CYS R 279 " - pdb=" SG CYS R 343 " distance=2.03 Simple disulfide: pdb=" SG CYS R 280 " - pdb=" SG CYS R 353 " distance=2.03 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " distance=2.03 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 9 " - pdb=" SG CYS Y 57 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 26 " - pdb=" SG CYS Y 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 34 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 38 " - pdb=" SG CYS Y 90 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 93 " - pdb=" SG CYS Y 100 " distance=2.04 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: 0.87 Conformation dependent library (CDL) restraints added in 615.7 milliseconds 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 18 sheets defined 32.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.563A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.637A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.600A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.631A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.526A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 241 through 245 removed outlier: 3.773A pdb=" N SER R 244 " --> pdb=" O GLY R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 265 Processing helix chain 'R' and resid 275 through 283 Processing helix chain 'R' and resid 359 through 373 removed outlier: 3.751A pdb=" N ARG R 363 " --> pdb=" O TYR R 359 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL R 364 " --> pdb=" O ASP R 360 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 386 Processing helix chain 'R' and resid 392 through 422 Processing helix chain 'R' and resid 425 through 435 removed outlier: 4.238A pdb=" N HIS R 429 " --> pdb=" O GLN R 425 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE R 431 " --> pdb=" O TYR R 427 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP R 432 " --> pdb=" O ASN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 470 removed outlier: 3.674A pdb=" N SER R 440 " --> pdb=" O GLY R 436 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 498 Processing helix chain 'R' and resid 499 through 504 removed outlier: 3.671A pdb=" N GLY R 504 " --> pdb=" O PRO R 501 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 554 Processing helix chain 'R' and resid 563 through 594 Proline residue: R 584 - end of helix Processing helix chain 'R' and resid 600 through 612 removed outlier: 3.634A pdb=" N LYS R 605 " --> pdb=" O VAL R 601 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL R 606 " --> pdb=" O THR R 602 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 624 Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 642 Processing helix chain 'X' and resid 40 through 45 removed outlier: 4.053A pdb=" N LYS X 45 " --> pdb=" O LEU X 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 213 through 214 removed outlier: 6.304A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.731A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.678A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.869A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.666A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.748A 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: 6.669A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.614A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.974A 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: 3.698A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 53 through 57 removed outlier: 3.755A pdb=" N SER R 81 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY R 220 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR R 197 " --> pdb=" O GLY R 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 53 through 57 removed outlier: 3.755A pdb=" N SER R 81 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU R 227 " --> pdb=" O ILE R 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 63 through 64 removed outlier: 4.370A pdb=" N ILE R 89 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 163 through 164 removed outlier: 3.558A pdb=" N ILE R 164 " --> pdb=" O GLU R 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 271 through 272 removed outlier: 6.905A pdb=" N ALA R 271 " --> pdb=" O ALA R 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'X' and resid 11 through 14 removed outlier: 3.728A pdb=" N GLY X 30 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS X 32 " --> pdb=" O CYS Y 38 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS Y 38 " --> pdb=" O CYS X 32 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS Y 34 " --> pdb=" O ALA X 36 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N THR Y 32 " --> pdb=" O PRO X 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 11 through 14 Processing sheet with id=AB7, first strand: chain 'X' and resid 59 through 69 removed outlier: 6.031A pdb=" N CYS X 60 " --> pdb=" O CYS X 84 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS X 84 " --> pdb=" O CYS X 60 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA X 62 " --> pdb=" O CYS X 82 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS X 82 " --> pdb=" O ALA X 62 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER X 64 " --> pdb=" O THR X 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 91 through 92 removed outlier: 3.660A pdb=" N SER X 92 " --> pdb=" O CYS Y 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'Y' and resid 56 through 68 removed outlier: 5.657A pdb=" N CYS Y 57 " --> pdb=" O CYS Y 90 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS Y 90 " --> pdb=" O CYS Y 57 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR Y 59 " --> pdb=" O CYS Y 88 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N CYS Y 88 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP Y 61 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1762 1.25 - 1.40: 2700 1.40 - 1.54: 6355 1.54 - 1.68: 136 1.68 - 1.83: 123 Bond restraints: 11076 Sorted by residual: bond pdb=" C33 55Z R 801 " pdb=" C34 55Z R 801 " ideal model delta sigma weight residual 1.517 1.300 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C30 55Z R 801 " pdb=" C31 55Z R 801 " ideal model delta sigma weight residual 1.516 1.319 0.197 2.00e-02 2.50e+03 9.67e+01 bond pdb=" C6 55Z R 801 " pdb=" O7 55Z R 801 " ideal model delta sigma weight residual 1.234 1.110 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C8 55Z R 801 " pdb=" C9 55Z R 801 " ideal model delta sigma weight residual 1.382 1.271 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C34 55Z R 801 " pdb=" N29 55Z R 801 " ideal model delta sigma weight residual 1.458 1.349 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 11071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 14914 3.37 - 6.74: 79 6.74 - 10.10: 17 10.10 - 13.47: 3 13.47 - 16.84: 2 Bond angle restraints: 15015 Sorted by residual: angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 112.38 98.44 13.94 1.22e+00 6.72e-01 1.31e+02 angle pdb=" CA ASP A 252 " pdb=" C ASP A 252 " pdb=" N TYR A 253 " ideal model delta sigma weight residual 115.89 103.49 12.40 1.40e+00 5.10e-01 7.85e+01 angle pdb=" C13 55Z R 801 " pdb=" S17 55Z R 801 " pdb=" C18 55Z R 801 " ideal model delta sigma weight residual 102.86 119.70 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" CA ASN A 254 " pdb=" C ASN A 254 " pdb=" O ASN A 254 " ideal model delta sigma weight residual 120.51 112.58 7.93 1.43e+00 4.89e-01 3.07e+01 angle pdb=" O ASP A 252 " pdb=" C ASP A 252 " pdb=" N TYR A 253 " ideal model delta sigma weight residual 122.43 128.93 -6.50 1.30e+00 5.92e-01 2.50e+01 ... (remaining 15010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6057 17.62 - 35.24: 530 35.24 - 52.85: 94 52.85 - 70.47: 18 70.47 - 88.09: 15 Dihedral angle restraints: 6714 sinusoidal: 2692 harmonic: 4022 Sorted by residual: dihedral pdb=" C ASN A 254 " pdb=" N ASN A 254 " pdb=" CA ASN A 254 " pdb=" CB ASN A 254 " ideal model delta harmonic sigma weight residual -122.60 -153.16 30.56 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" N ASN A 254 " pdb=" C ASN A 254 " pdb=" CA ASN A 254 " pdb=" CB ASN A 254 " ideal model delta harmonic sigma weight residual 122.80 152.93 -30.13 0 2.50e+00 1.60e-01 1.45e+02 dihedral pdb=" CB CYS X 10 " pdb=" SG CYS X 10 " pdb=" SG CYS X 60 " pdb=" CB CYS X 60 " ideal model delta sinusoidal sigma weight residual 93.00 168.78 -75.78 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 6711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 1711 0.247 - 0.495: 2 0.495 - 0.742: 0 0.742 - 0.989: 0 0.989 - 1.236: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" CA ASN A 254 " pdb=" N ASN A 254 " pdb=" C ASN A 254 " pdb=" CB ASN A 254 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CA ARG A 255 " pdb=" N ARG A 255 " pdb=" C ARG A 255 " pdb=" CB ARG A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA CYS X 84 " pdb=" N CYS X 84 " pdb=" C CYS X 84 " pdb=" CB CYS X 84 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1711 not shown) Planarity restraints: 1917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 252 " -0.034 2.00e-02 2.50e+03 7.69e-02 5.91e+01 pdb=" C ASP A 252 " 0.133 2.00e-02 2.50e+03 pdb=" O ASP A 252 " -0.055 2.00e-02 2.50e+03 pdb=" N TYR A 253 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 354 " 0.018 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" CD GLU R 354 " -0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU R 354 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU R 354 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 55Z R 801 " -0.005 2.00e-02 2.50e+03 1.78e-02 1.03e+01 pdb=" C11 55Z R 801 " -0.007 2.00e-02 2.50e+03 pdb=" C13 55Z R 801 " -0.015 2.00e-02 2.50e+03 pdb=" C15 55Z R 801 " -0.001 2.00e-02 2.50e+03 pdb=" C19 55Z R 801 " 0.021 2.00e-02 2.50e+03 pdb=" C6 55Z R 801 " 0.044 2.00e-02 2.50e+03 pdb=" C8 55Z R 801 " -0.025 2.00e-02 2.50e+03 pdb=" C9 55Z R 801 " -0.018 2.00e-02 2.50e+03 pdb=" N12 55Z R 801 " 0.004 2.00e-02 2.50e+03 pdb=" N14 55Z R 801 " -0.003 2.00e-02 2.50e+03 pdb=" N35 55Z R 801 " -0.013 2.00e-02 2.50e+03 pdb=" S16 55Z R 801 " -0.001 2.00e-02 2.50e+03 pdb=" S17 55Z R 801 " 0.017 2.00e-02 2.50e+03 ... (remaining 1914 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 114 2.55 - 3.14: 9019 3.14 - 3.72: 16588 3.72 - 4.31: 22348 4.31 - 4.90: 38527 Nonbonded interactions: 86596 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 1.962 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.079 3.040 nonbonded pdb=" O ASP R 518 " pdb=" OG SER R 524 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR R 359 " pdb=" OD1 ASN R 603 " model vdw 2.128 3.040 nonbonded pdb=" ND2 ASN R 507 " pdb=" OD2 ASP R 518 " model vdw 2.160 3.120 ... (remaining 86591 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 11091 Z= 0.280 Angle : 0.766 16.837 15045 Z= 0.437 Chirality : 0.052 1.236 1714 Planarity : 0.005 0.077 1917 Dihedral : 13.977 88.091 4065 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 0.17 % Allowed : 0.33 % Favored : 99.50 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.51 % 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: -0.18 (0.24), residues: 1365 helix: 1.38 (0.27), residues: 385 sheet: -1.69 (0.28), residues: 301 loop : -0.11 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 346 TYR 0.032 0.001 TYR R 389 PHE 0.013 0.001 PHE B 234 TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00543 (11076) covalent geometry : angle 0.75976 (15015) SS BOND : bond 0.00532 ( 15) SS BOND : angle 2.26265 ( 30) hydrogen bonds : bond 0.15466 ( 449) hydrogen bonds : angle 6.72350 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7711 (t0) cc_final: 0.7453 (t0) REVERT: A 273 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7797 (ttm-80) REVERT: B 127 LYS cc_start: 0.7346 (mttp) cc_final: 0.6987 (mttp) REVERT: B 315 VAL cc_start: 0.8258 (t) cc_final: 0.8006 (p) REVERT: R 228 ASP cc_start: 0.7393 (t0) cc_final: 0.7172 (t0) REVERT: X 29 MET cc_start: 0.4549 (mtm) cc_final: 0.4333 (mtm) REVERT: X 46 THR cc_start: 0.7606 (m) cc_final: 0.7380 (t) REVERT: Y 7 PRO cc_start: 0.6142 (Cg_endo) cc_final: 0.5904 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.1225 time to fit residues: 48.7745 Evaluate side-chains 249 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 158 ASN ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 GLN R 615 ASN Y 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.137135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.124059 restraints weight = 21515.736| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.58 r_work: 0.3720 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11091 Z= 0.144 Angle : 0.667 8.501 15045 Z= 0.348 Chirality : 0.046 0.181 1714 Planarity : 0.005 0.058 1917 Dihedral : 5.441 41.690 1526 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.92 % Allowed : 10.36 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.06 (0.23), residues: 1365 helix: 1.62 (0.26), residues: 408 sheet: -1.38 (0.28), residues: 301 loop : -0.15 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.020 0.002 TYR R 389 PHE 0.012 0.001 PHE R 403 TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS R 429 Details of bonding type rmsd covalent geometry : bond 0.00320 (11076) covalent geometry : angle 0.66476 (15015) SS BOND : bond 0.00466 ( 15) SS BOND : angle 1.46890 ( 30) hydrogen bonds : bond 0.04433 ( 449) hydrogen bonds : angle 4.84233 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 301 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7937 (tp30) cc_final: 0.7334 (tp30) REVERT: A 51 SER cc_start: 0.8192 (p) cc_final: 0.7937 (m) REVERT: A 249 ASP cc_start: 0.7965 (t70) cc_final: 0.7710 (t0) REVERT: A 262 ASP cc_start: 0.7999 (t0) cc_final: 0.7544 (t0) REVERT: A 265 SER cc_start: 0.8958 (t) cc_final: 0.8745 (t) REVERT: A 285 ASP cc_start: 0.6977 (p0) cc_final: 0.6168 (t0) REVERT: B 51 LEU cc_start: 0.8952 (mp) cc_final: 0.8748 (mp) REVERT: B 76 ASP cc_start: 0.8043 (p0) cc_final: 0.7787 (p0) REVERT: B 126 LEU cc_start: 0.8763 (mt) cc_final: 0.8432 (mt) REVERT: B 163 ASP cc_start: 0.8051 (t70) cc_final: 0.7677 (t0) REVERT: B 175 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7449 (mm-40) REVERT: B 200 VAL cc_start: 0.9063 (m) cc_final: 0.8796 (p) REVERT: B 315 VAL cc_start: 0.8231 (t) cc_final: 0.7930 (p) REVERT: R 81 SER cc_start: 0.8670 (p) cc_final: 0.8298 (t) REVERT: R 108 THR cc_start: 0.7996 (m) cc_final: 0.7149 (p) REVERT: R 203 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: R 342 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7966 (ptp-110) REVERT: R 553 VAL cc_start: 0.8463 (t) cc_final: 0.8164 (p) REVERT: R 559 MET cc_start: 0.5801 (tpt) cc_final: 0.5238 (tpt) REVERT: R 571 MET cc_start: 0.7781 (mtp) cc_final: 0.7516 (mtp) outliers start: 23 outliers final: 10 residues processed: 308 average time/residue: 0.1110 time to fit residues: 46.5666 Evaluate side-chains 287 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 276 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 203 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain R residue 628 LYS Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Y residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 236 GLN A 380 GLN B 156 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN ** R 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116637 restraints weight = 21440.942| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.56 r_work: 0.3617 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11091 Z= 0.203 Angle : 0.683 9.594 15045 Z= 0.362 Chirality : 0.047 0.196 1714 Planarity : 0.005 0.056 1917 Dihedral : 5.568 35.974 1524 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.84 % Allowed : 14.95 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.03 (0.23), residues: 1365 helix: 1.72 (0.26), residues: 400 sheet: -1.33 (0.28), residues: 301 loop : -0.36 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 70 TYR 0.017 0.002 TYR A 301 PHE 0.015 0.002 PHE R 403 TRP 0.016 0.002 TRP B 82 HIS 0.007 0.002 HIS R 192 Details of bonding type rmsd covalent geometry : bond 0.00456 (11076) covalent geometry : angle 0.67702 (15015) SS BOND : bond 0.00927 ( 15) SS BOND : angle 2.20312 ( 30) hydrogen bonds : bond 0.04725 ( 449) hydrogen bonds : angle 4.66109 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8070 (tp30) cc_final: 0.7479 (tp30) REVERT: A 233 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7485 (tppp) REVERT: A 262 ASP cc_start: 0.8030 (t0) cc_final: 0.7708 (t0) REVERT: A 265 SER cc_start: 0.9028 (t) cc_final: 0.8814 (t) REVERT: A 267 TRP cc_start: 0.8764 (t-100) cc_final: 0.8092 (t-100) REVERT: A 269 ASN cc_start: 0.8748 (t0) cc_final: 0.8548 (t0) REVERT: A 275 ILE cc_start: 0.8739 (mm) cc_final: 0.8533 (mt) REVERT: B 51 LEU cc_start: 0.8958 (mp) cc_final: 0.8754 (mp) REVERT: B 175 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7733 (mm-40) REVERT: B 189 SER cc_start: 0.8100 (p) cc_final: 0.7694 (t) REVERT: B 214 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7968 (mtt90) REVERT: B 259 GLN cc_start: 0.7962 (pt0) cc_final: 0.7757 (pt0) REVERT: B 315 VAL cc_start: 0.8225 (t) cc_final: 0.7997 (p) REVERT: R 81 SER cc_start: 0.8578 (p) cc_final: 0.8378 (t) REVERT: R 108 THR cc_start: 0.8292 (m) cc_final: 0.7583 (p) REVERT: R 121 ASN cc_start: 0.7005 (t0) cc_final: 0.6640 (m-40) REVERT: R 253 SER cc_start: 0.8694 (t) cc_final: 0.8480 (t) REVERT: R 377 ASN cc_start: 0.7471 (m-40) cc_final: 0.7108 (t0) REVERT: R 405 ASP cc_start: 0.8274 (m-30) cc_final: 0.7971 (t0) REVERT: R 419 ASP cc_start: 0.7897 (t0) cc_final: 0.7616 (t0) REVERT: R 484 ILE cc_start: 0.8685 (mm) cc_final: 0.8302 (tp) REVERT: R 582 MET cc_start: 0.7658 (tmm) cc_final: 0.7422 (tmm) outliers start: 34 outliers final: 20 residues processed: 300 average time/residue: 0.1092 time to fit residues: 45.1453 Evaluate side-chains 275 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 517 MET Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 26 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 119 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 239 ASN A 380 GLN B 44 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.130224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.117589 restraints weight = 21241.844| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.55 r_work: 0.3628 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11091 Z= 0.136 Angle : 0.643 11.220 15045 Z= 0.335 Chirality : 0.045 0.190 1714 Planarity : 0.004 0.055 1917 Dihedral : 5.364 38.274 1524 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.01 % Allowed : 16.96 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.08 (0.23), residues: 1365 helix: 1.86 (0.26), residues: 402 sheet: -1.33 (0.28), residues: 300 loop : -0.31 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 42 TYR 0.016 0.001 TYR B 105 PHE 0.027 0.001 PHE R 493 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00306 (11076) covalent geometry : angle 0.63417 (15015) SS BOND : bond 0.00293 ( 15) SS BOND : angle 2.47239 ( 30) hydrogen bonds : bond 0.04215 ( 449) hydrogen bonds : angle 4.44391 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7226 (ttm) cc_final: 0.6917 (mtt) REVERT: A 27 GLU cc_start: 0.8073 (tp30) cc_final: 0.7467 (tp30) REVERT: A 262 ASP cc_start: 0.7948 (t0) cc_final: 0.7672 (t0) REVERT: A 267 TRP cc_start: 0.8767 (t-100) cc_final: 0.8088 (t-100) REVERT: A 269 ASN cc_start: 0.8739 (t0) cc_final: 0.8536 (t0) REVERT: A 360 GLU cc_start: 0.7913 (mp0) cc_final: 0.7544 (mp0) REVERT: B 155 ASN cc_start: 0.8470 (t0) cc_final: 0.8265 (t0) REVERT: B 175 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7564 (mm-40) REVERT: B 189 SER cc_start: 0.7870 (p) cc_final: 0.7318 (t) REVERT: B 214 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7967 (mtt90) REVERT: B 254 ASP cc_start: 0.7804 (t0) cc_final: 0.7566 (t0) REVERT: B 259 GLN cc_start: 0.7787 (pt0) cc_final: 0.7549 (pt0) REVERT: B 315 VAL cc_start: 0.8171 (t) cc_final: 0.7941 (p) REVERT: R 108 THR cc_start: 0.8123 (m) cc_final: 0.7401 (p) REVERT: R 121 ASN cc_start: 0.7036 (t0) cc_final: 0.6588 (m-40) REVERT: R 245 ILE cc_start: 0.8139 (tt) cc_final: 0.7922 (mt) REVERT: R 253 SER cc_start: 0.8735 (t) cc_final: 0.8524 (t) REVERT: R 377 ASN cc_start: 0.7464 (m-40) cc_final: 0.7216 (t0) REVERT: R 398 MET cc_start: 0.8066 (tpp) cc_final: 0.7684 (tpp) REVERT: R 402 SER cc_start: 0.8338 (t) cc_final: 0.8034 (t) REVERT: R 419 ASP cc_start: 0.7927 (t0) cc_final: 0.7626 (t0) REVERT: R 553 VAL cc_start: 0.8540 (t) cc_final: 0.8253 (p) outliers start: 36 outliers final: 16 residues processed: 286 average time/residue: 0.1111 time to fit residues: 43.3974 Evaluate side-chains 272 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 256 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain Y residue 26 CYS Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.0570 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.129652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.117099 restraints weight = 21248.139| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.55 r_work: 0.3610 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11091 Z= 0.129 Angle : 0.637 11.887 15045 Z= 0.331 Chirality : 0.045 0.188 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.214 33.950 1524 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.26 % Allowed : 18.46 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.10 (0.23), residues: 1365 helix: 1.94 (0.26), residues: 402 sheet: -1.30 (0.28), residues: 299 loop : -0.36 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 375 TYR 0.014 0.001 TYR B 105 PHE 0.027 0.001 PHE R 493 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00291 (11076) covalent geometry : angle 0.62949 (15015) SS BOND : bond 0.00386 ( 15) SS BOND : angle 2.20608 ( 30) hydrogen bonds : bond 0.04070 ( 449) hydrogen bonds : angle 4.31638 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7220 (ttm) cc_final: 0.6952 (mtt) REVERT: A 27 GLU cc_start: 0.8038 (tp30) cc_final: 0.7381 (tp30) REVERT: A 262 ASP cc_start: 0.8041 (t0) cc_final: 0.7735 (t0) REVERT: A 267 TRP cc_start: 0.8803 (t-100) cc_final: 0.8387 (t-100) REVERT: A 360 GLU cc_start: 0.7883 (mp0) cc_final: 0.7583 (mp0) REVERT: A 379 ARG cc_start: 0.8404 (ttm110) cc_final: 0.7737 (mtm110) REVERT: B 155 ASN cc_start: 0.8429 (t0) cc_final: 0.7663 (t0) REVERT: B 189 SER cc_start: 0.8089 (p) cc_final: 0.7593 (t) REVERT: B 259 GLN cc_start: 0.7861 (pt0) cc_final: 0.7624 (pt0) REVERT: B 291 ASP cc_start: 0.6968 (t0) cc_final: 0.6715 (t70) REVERT: B 293 ASN cc_start: 0.8757 (p0) cc_final: 0.8291 (p0) REVERT: B 315 VAL cc_start: 0.8130 (t) cc_final: 0.7899 (p) REVERT: R 108 THR cc_start: 0.7927 (m) cc_final: 0.7260 (p) REVERT: R 398 MET cc_start: 0.7997 (tpp) cc_final: 0.7665 (tpp) REVERT: R 402 SER cc_start: 0.8308 (t) cc_final: 0.7985 (t) REVERT: R 405 ASP cc_start: 0.8006 (m-30) cc_final: 0.7649 (t0) REVERT: R 553 VAL cc_start: 0.8569 (t) cc_final: 0.8319 (p) REVERT: R 612 TYR cc_start: 0.8875 (t80) cc_final: 0.8612 (t80) REVERT: X 12 LEU cc_start: 0.6268 (mp) cc_final: 0.5979 (mp) REVERT: Y 72 CYS cc_start: -0.1325 (OUTLIER) cc_final: -0.2163 (p) outliers start: 27 outliers final: 20 residues processed: 281 average time/residue: 0.1072 time to fit residues: 41.3224 Evaluate side-chains 276 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 123 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.0060 chunk 73 optimal weight: 0.0070 chunk 101 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 44 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.3864 r_free = 0.3864 target = 0.128322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115868 restraints weight = 21176.055| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.56 r_work: 0.3592 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11091 Z= 0.151 Angle : 0.664 10.452 15045 Z= 0.342 Chirality : 0.046 0.210 1714 Planarity : 0.004 0.056 1917 Dihedral : 5.355 46.815 1524 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.84 % Allowed : 20.05 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.12 (0.23), residues: 1365 helix: 1.96 (0.26), residues: 402 sheet: -1.18 (0.29), residues: 287 loop : -0.43 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 346 TYR 0.021 0.001 TYR B 105 PHE 0.025 0.001 PHE R 493 TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00348 (11076) covalent geometry : angle 0.65836 (15015) SS BOND : bond 0.00334 ( 15) SS BOND : angle 2.02497 ( 30) hydrogen bonds : bond 0.04217 ( 449) hydrogen bonds : angle 4.31209 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 269 time to evaluate : 0.363 Fit side-chains REVERT: A 25 MET cc_start: 0.7287 (ttm) cc_final: 0.7040 (mtt) REVERT: A 27 GLU cc_start: 0.8095 (tp30) cc_final: 0.7431 (tp30) REVERT: A 262 ASP cc_start: 0.7988 (t0) cc_final: 0.7697 (t0) REVERT: A 267 TRP cc_start: 0.8797 (t-100) cc_final: 0.7970 (t-100) REVERT: A 360 GLU cc_start: 0.7906 (mp0) cc_final: 0.7620 (mp0) REVERT: A 379 ARG cc_start: 0.8423 (ttm110) cc_final: 0.8207 (mtm-85) REVERT: B 155 ASN cc_start: 0.8461 (t0) cc_final: 0.7757 (t0) REVERT: B 163 ASP cc_start: 0.8073 (t70) cc_final: 0.7712 (t0) REVERT: B 189 SER cc_start: 0.8106 (p) cc_final: 0.7669 (t) REVERT: B 259 GLN cc_start: 0.7967 (pt0) cc_final: 0.7730 (pt0) REVERT: B 293 ASN cc_start: 0.8697 (p0) cc_final: 0.8100 (p0) REVERT: B 315 VAL cc_start: 0.8124 (t) cc_final: 0.7903 (p) REVERT: R 108 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7284 (p) REVERT: R 253 SER cc_start: 0.8890 (t) cc_final: 0.8394 (p) REVERT: R 419 ASP cc_start: 0.7869 (t0) cc_final: 0.7585 (t0) REVERT: R 612 TYR cc_start: 0.8835 (t80) cc_final: 0.8589 (t80) outliers start: 34 outliers final: 21 residues processed: 288 average time/residue: 0.1149 time to fit residues: 45.3173 Evaluate side-chains 271 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 122 optimal weight: 0.0370 chunk 101 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 106 GLN R 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.128080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115748 restraints weight = 21250.626| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.56 r_work: 0.3590 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11091 Z= 0.143 Angle : 0.660 9.453 15045 Z= 0.342 Chirality : 0.045 0.181 1714 Planarity : 0.004 0.056 1917 Dihedral : 5.321 46.677 1524 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.67 % Allowed : 20.80 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.14 (0.23), residues: 1365 helix: 2.04 (0.26), residues: 401 sheet: -1.24 (0.29), residues: 297 loop : -0.40 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 346 TYR 0.019 0.001 TYR B 105 PHE 0.025 0.001 PHE R 493 TRP 0.018 0.002 TRP B 169 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00325 (11076) covalent geometry : angle 0.65488 (15015) SS BOND : bond 0.00411 ( 15) SS BOND : angle 1.87345 ( 30) hydrogen bonds : bond 0.04157 ( 449) hydrogen bonds : angle 4.32884 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.369 Fit side-chains REVERT: A 25 MET cc_start: 0.7265 (ttm) cc_final: 0.7037 (mtt) REVERT: A 27 GLU cc_start: 0.8136 (tp30) cc_final: 0.7453 (tp30) REVERT: A 262 ASP cc_start: 0.8051 (t0) cc_final: 0.7749 (t0) REVERT: A 267 TRP cc_start: 0.8778 (t-100) cc_final: 0.8223 (t-100) REVERT: A 270 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7714 (ttp80) REVERT: A 346 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7621 (ttm110) REVERT: A 360 GLU cc_start: 0.7872 (mp0) cc_final: 0.7598 (mp0) REVERT: B 86 THR cc_start: 0.8468 (p) cc_final: 0.8255 (p) REVERT: B 130 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6088 (mt-10) REVERT: B 155 ASN cc_start: 0.8532 (t0) cc_final: 0.7753 (t0) REVERT: B 189 SER cc_start: 0.8140 (p) cc_final: 0.7704 (t) REVERT: B 214 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7928 (mtt90) REVERT: B 259 GLN cc_start: 0.7957 (pt0) cc_final: 0.7692 (pt0) REVERT: B 293 ASN cc_start: 0.8701 (p0) cc_final: 0.8083 (p0) REVERT: B 315 VAL cc_start: 0.8039 (t) cc_final: 0.7787 (p) REVERT: G 38 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6418 (ttp) REVERT: R 108 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7283 (p) REVERT: R 253 SER cc_start: 0.8893 (t) cc_final: 0.8395 (p) REVERT: R 405 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7820 (t70) outliers start: 32 outliers final: 26 residues processed: 291 average time/residue: 0.1083 time to fit residues: 43.2588 Evaluate side-chains 284 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 356 ILE Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 34 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 16 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.0000 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 126 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN R 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.129710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.117394 restraints weight = 21219.928| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.57 r_work: 0.3611 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11091 Z= 0.121 Angle : 0.665 10.622 15045 Z= 0.336 Chirality : 0.045 0.182 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.173 48.316 1524 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 21.39 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.21 (0.23), residues: 1365 helix: 2.06 (0.26), residues: 403 sheet: -1.19 (0.29), residues: 296 loop : -0.35 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 379 TYR 0.018 0.001 TYR B 105 PHE 0.023 0.001 PHE R 493 TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00269 (11076) covalent geometry : angle 0.66094 (15015) SS BOND : bond 0.00282 ( 15) SS BOND : angle 1.68969 ( 30) hydrogen bonds : bond 0.03911 ( 449) hydrogen bonds : angle 4.29720 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.7251 (ttm) cc_final: 0.7010 (mtt) REVERT: A 27 GLU cc_start: 0.8184 (tp30) cc_final: 0.7921 (tp30) REVERT: A 229 ASP cc_start: 0.8366 (p0) cc_final: 0.8059 (p0) REVERT: A 262 ASP cc_start: 0.8077 (t0) cc_final: 0.7769 (t0) REVERT: A 267 TRP cc_start: 0.8764 (t-100) cc_final: 0.8234 (t-100) REVERT: A 270 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7659 (ttp80) REVERT: A 333 ASP cc_start: 0.8154 (t0) cc_final: 0.7862 (t0) REVERT: A 360 GLU cc_start: 0.7835 (mp0) cc_final: 0.7564 (mp0) REVERT: B 86 THR cc_start: 0.8452 (p) cc_final: 0.8241 (p) REVERT: B 130 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6026 (mt-10) REVERT: B 155 ASN cc_start: 0.8490 (t0) cc_final: 0.7682 (t0) REVERT: B 163 ASP cc_start: 0.8114 (t70) cc_final: 0.7775 (t0) REVERT: B 189 SER cc_start: 0.8172 (p) cc_final: 0.7709 (t) REVERT: B 214 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7835 (mtt90) REVERT: B 293 ASN cc_start: 0.8578 (p0) cc_final: 0.8357 (p0) REVERT: B 315 VAL cc_start: 0.7967 (t) cc_final: 0.7695 (p) REVERT: R 108 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7272 (p) REVERT: R 253 SER cc_start: 0.8876 (t) cc_final: 0.8328 (p) REVERT: R 405 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7832 (t70) REVERT: R 518 ASP cc_start: 0.7557 (t0) cc_final: 0.7349 (t0) REVERT: R 520 GLU cc_start: 0.8263 (mp0) cc_final: 0.7845 (mp0) REVERT: Y 72 CYS cc_start: -0.1812 (OUTLIER) cc_final: -0.2769 (p) outliers start: 34 outliers final: 26 residues processed: 281 average time/residue: 0.1073 time to fit residues: 41.3573 Evaluate side-chains 286 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 263 GLU Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 239 ASN B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN R 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.128287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115977 restraints weight = 20976.728| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.56 r_work: 0.3592 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11091 Z= 0.142 Angle : 0.680 9.166 15045 Z= 0.348 Chirality : 0.045 0.167 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.206 48.388 1524 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.51 % Allowed : 22.22 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.16 (0.23), residues: 1365 helix: 2.03 (0.26), residues: 402 sheet: -1.25 (0.29), residues: 297 loop : -0.36 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 13 TYR 0.017 0.001 TYR B 105 PHE 0.021 0.001 PHE R 493 TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00325 (11076) covalent geometry : angle 0.67599 (15015) SS BOND : bond 0.00286 ( 15) SS BOND : angle 1.81896 ( 30) hydrogen bonds : bond 0.04036 ( 449) hydrogen bonds : angle 4.33087 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 0.317 Fit side-chains REVERT: A 25 MET cc_start: 0.7283 (ttm) cc_final: 0.7053 (mtt) REVERT: A 27 GLU cc_start: 0.8215 (tp30) cc_final: 0.7955 (tp30) REVERT: A 229 ASP cc_start: 0.8330 (p0) cc_final: 0.7957 (p0) REVERT: A 262 ASP cc_start: 0.8086 (t0) cc_final: 0.7765 (t0) REVERT: A 267 TRP cc_start: 0.8789 (t-100) cc_final: 0.8310 (t-100) REVERT: A 270 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7740 (ttp80) REVERT: A 334 GLU cc_start: 0.7927 (tp30) cc_final: 0.7713 (tp30) REVERT: A 360 GLU cc_start: 0.7915 (mp0) cc_final: 0.7636 (mp0) REVERT: B 86 THR cc_start: 0.8474 (p) cc_final: 0.8266 (p) REVERT: B 130 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6101 (mt-10) REVERT: B 155 ASN cc_start: 0.8488 (t0) cc_final: 0.7725 (t0) REVERT: B 163 ASP cc_start: 0.8173 (t70) cc_final: 0.7752 (t0) REVERT: B 189 SER cc_start: 0.8203 (p) cc_final: 0.7765 (t) REVERT: B 293 ASN cc_start: 0.8496 (p0) cc_final: 0.8253 (p0) REVERT: B 315 VAL cc_start: 0.7956 (t) cc_final: 0.7689 (p) REVERT: G 58 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7552 (mp0) REVERT: R 108 THR cc_start: 0.7895 (m) cc_final: 0.7334 (p) REVERT: R 253 SER cc_start: 0.8923 (t) cc_final: 0.8394 (p) REVERT: R 405 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7818 (t70) REVERT: R 518 ASP cc_start: 0.7611 (t0) cc_final: 0.7328 (t0) REVERT: R 520 GLU cc_start: 0.8250 (mp0) cc_final: 0.7828 (mp0) REVERT: Y 104 LYS cc_start: 0.6262 (tptp) cc_final: 0.5473 (tttt) outliers start: 30 outliers final: 27 residues processed: 293 average time/residue: 0.1039 time to fit residues: 42.0729 Evaluate side-chains 287 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 263 GLU Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 34 CYS Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 134 optimal weight: 0.0770 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.117027 restraints weight = 21048.226| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.58 r_work: 0.3615 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11091 Z= 0.120 Angle : 0.672 10.739 15045 Z= 0.340 Chirality : 0.044 0.179 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.074 49.015 1524 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.51 % Allowed : 23.22 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.19 (0.23), residues: 1365 helix: 2.06 (0.26), residues: 402 sheet: -1.25 (0.29), residues: 297 loop : -0.35 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 13 TYR 0.018 0.001 TYR R 182 PHE 0.021 0.001 PHE R 493 TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00270 (11076) covalent geometry : angle 0.66887 (15015) SS BOND : bond 0.00284 ( 15) SS BOND : angle 1.66393 ( 30) hydrogen bonds : bond 0.03837 ( 449) hydrogen bonds : angle 4.29444 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 260 time to evaluate : 0.386 Fit side-chains REVERT: A 25 MET cc_start: 0.7291 (ttm) cc_final: 0.7080 (mtt) REVERT: A 27 GLU cc_start: 0.8226 (tp30) cc_final: 0.7969 (tp30) REVERT: A 262 ASP cc_start: 0.8065 (t0) cc_final: 0.7716 (t0) REVERT: A 267 TRP cc_start: 0.8762 (t-100) cc_final: 0.8332 (t-100) REVERT: A 270 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7675 (ttp80) REVERT: A 307 ARG cc_start: 0.6808 (mmp80) cc_final: 0.6422 (mmp80) REVERT: A 334 GLU cc_start: 0.7899 (tp30) cc_final: 0.7682 (tp30) REVERT: B 86 THR cc_start: 0.8425 (p) cc_final: 0.8212 (p) REVERT: B 130 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6114 (mt-10) REVERT: B 155 ASN cc_start: 0.8441 (t0) cc_final: 0.7661 (t0) REVERT: B 163 ASP cc_start: 0.8106 (t70) cc_final: 0.7767 (t0) REVERT: B 189 SER cc_start: 0.8243 (p) cc_final: 0.7769 (t) REVERT: B 293 ASN cc_start: 0.8351 (p0) cc_final: 0.8114 (p0) REVERT: B 315 VAL cc_start: 0.7882 (t) cc_final: 0.7584 (p) REVERT: G 13 ARG cc_start: 0.8286 (ptp90) cc_final: 0.7914 (mpp80) REVERT: G 58 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7487 (mp0) REVERT: R 108 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7238 (p) REVERT: R 253 SER cc_start: 0.8873 (t) cc_final: 0.8635 (t) REVERT: R 398 MET cc_start: 0.8190 (tpp) cc_final: 0.7700 (tpp) REVERT: R 405 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7798 (t70) REVERT: R 520 GLU cc_start: 0.8217 (mp0) cc_final: 0.7877 (mp0) REVERT: Y 104 LYS cc_start: 0.6180 (tptp) cc_final: 0.5416 (tttt) outliers start: 30 outliers final: 24 residues processed: 276 average time/residue: 0.1090 time to fit residues: 41.2022 Evaluate side-chains 288 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 263 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 356 ILE Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 34 CYS Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 117 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 239 ASN B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.128481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.116112 restraints weight = 21089.373| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.56 r_work: 0.3602 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11091 Z= 0.134 Angle : 0.684 12.297 15045 Z= 0.348 Chirality : 0.045 0.187 1714 Planarity : 0.005 0.057 1917 Dihedral : 5.084 49.122 1524 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.59 % Allowed : 23.31 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.22 (0.23), residues: 1365 helix: 2.08 (0.26), residues: 402 sheet: -1.18 (0.29), residues: 302 loop : -0.33 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 13 TYR 0.019 0.001 TYR R 182 PHE 0.021 0.001 PHE R 493 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS R 160 Details of bonding type rmsd covalent geometry : bond 0.00307 (11076) covalent geometry : angle 0.68021 (15015) SS BOND : bond 0.00285 ( 15) SS BOND : angle 1.69216 ( 30) hydrogen bonds : bond 0.03912 ( 449) hydrogen bonds : angle 4.31111 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.20 seconds wall clock time: 41 minutes 48.78 seconds (2508.78 seconds total)