Starting phenix.real_space_refine on Fri Jul 3 02:51:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axl_43969/07_2026/9axl_43969_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axl_43969/07_2026/9axl_43969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axl_43969/07_2026/9axl_43969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axl_43969/07_2026/9axl_43969.map" model { file = "/net/cci-nas-00/data/ceres_data/9axl_43969/07_2026/9axl_43969_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axl_43969/07_2026/9axl_43969_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 72 5.16 5 C 7355 2.51 5 N 2009 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 591, 4484 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 36, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 591, 4484 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 36, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 4561 Chain: "B" Number of atoms: 3885 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 524, 3881 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 494} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 104 Conformer: "B" Number of residues, atoms: 524, 3881 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 494} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 104 bond proxies already assigned to first conformer: 3942 Chain: "H" Number of atoms: 1698 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1681 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 213} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 227, 1681 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 213} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 1706 Chain: "L" Number of atoms: 1637 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1637 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 8 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 7} Link IDs: {None: 7} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 276 " occ=0.73 ... (20 atoms not shown) pdb=" NH2BARG A 276 " occ=0.27 residue: pdb=" N AHIS A 587 " occ=0.67 ... (18 atoms not shown) pdb=" NE2BHIS A 587 " occ=0.33 residue: pdb=" N AARG H 98 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG H 98 " occ=0.57 residue: pdb=" N CYS L 213 " occ=0.00 ... (5 atoms not shown) pdb=" OXT CYS L 213 " occ=0.00 Time building chain proxies: 4.31, per 1000 atoms: 0.37 Number of scatterers: 11748 At special positions: 0 Unit cell: (86, 105.78, 190.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 72 16.00 Mg 1 11.99 O 2305 8.00 N 2009 7.00 C 7355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.04 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG ACYS L 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 918.5 milliseconds 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 30 sheets defined 12.6% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.723A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.048A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.692A pdb=" N ARG A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 removed outlier: 3.888A pdb=" N ARG B 8 " --> pdb=" O CYS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.483A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 121 through 130 removed outlier: 5.280A pdb=" N ASP B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 127 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 removed outlier: 3.698A pdb=" N LYS B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.585A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 3.961A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.654A pdb=" N SER B 284 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 Processing helix chain 'B' and resid 312 through 323 removed outlier: 4.632A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.926A pdb=" N LYS B 354 " --> pdb=" O LYS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 removed outlier: 3.587A pdb=" N ALA B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 removed outlier: 3.648A pdb=" N SER B 496 " --> pdb=" O PRO B 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.564A pdb=" N THR A 9 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79 removed outlier: 3.500A pdb=" N GLU A 75 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.831A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.804A pdb=" N SER A 172 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.662A pdb=" N HIS A 278 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.542A pdb=" N LEU A 345 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 6.165A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 523 removed outlier: 5.322A pdb=" N VAL A 454 " --> pdb=" O AHIS A 587 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 530 through 536 Processing sheet with id=AB5, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.236A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.681A pdb=" N ALA B 372 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.680A pdb=" N LEU B 194 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 196 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE B 151 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 116 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 311 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 333 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL B 310 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 454 through 456 removed outlier: 3.533A pdb=" N GLU B 456 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.834A pdb=" N CYS B 473 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 499 through 501 Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.697A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.171A pdb=" N TYR H 187 " --> pdb=" O GLY H 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.171A pdb=" N TYR H 187 " --> pdb=" O GLY H 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 165 through 166 removed outlier: 3.678A pdb=" N THR H 165 " --> pdb=" O ASN H 208 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.666A pdb=" N THR L 5 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER L 66 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.615A pdb=" N ALA L 13 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AD2, first strand: chain 'L' and resid 113 through 117 removed outlier: 5.893A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 144 through 149 411 hydrogen bonds defined for protein. 1034 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: 1.75 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.19: 1 1.19 - 1.52: 10305 1.52 - 1.86: 1696 1.86 - 2.20: 0 2.20 - 2.54: 1 Bond restraints: 12003 Sorted by residual: bond pdb=" CB PRO B 363 " pdb=" CG PRO B 363 " ideal model delta sigma weight residual 1.492 2.539 -1.047 5.00e-02 4.00e+02 4.39e+02 bond pdb=" CG PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 1.503 0.849 0.654 3.40e-02 8.65e+02 3.70e+02 bond pdb=" N PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.16e+01 bond pdb=" CA PRO B 363 " pdb=" CB PRO B 363 " ideal model delta sigma weight residual 1.535 1.437 0.099 1.60e-02 3.91e+03 3.81e+01 bond pdb=" N PRO B 363 " pdb=" CA PRO B 363 " ideal model delta sigma weight residual 1.464 1.419 0.044 9.30e-03 1.16e+04 2.27e+01 ... (remaining 11998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.86: 16339 15.86 - 31.72: 3 31.72 - 47.58: 0 47.58 - 63.44: 0 63.44 - 79.30: 1 Bond angle restraints: 16343 Sorted by residual: angle pdb=" CB PRO B 363 " pdb=" CG PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 106.10 26.80 79.30 3.20e+00 9.77e-02 6.14e+02 angle pdb=" CA PRO B 363 " pdb=" CB PRO B 363 " pdb=" CG PRO B 363 " ideal model delta sigma weight residual 104.50 76.10 28.40 1.90e+00 2.77e-01 2.23e+02 angle pdb=" N PRO B 363 " pdb=" CD PRO B 363 " pdb=" CG PRO B 363 " ideal model delta sigma weight residual 103.20 82.68 20.52 1.50e+00 4.44e-01 1.87e+02 angle pdb=" N PRO B 363 " pdb=" CA PRO B 363 " pdb=" CB PRO B 363 " ideal model delta sigma weight residual 102.72 89.52 13.20 1.16e+00 7.43e-01 1.29e+02 angle pdb=" CA PRO B 363 " pdb=" N PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.02e+02 ... (remaining 16338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.83: 6612 22.83 - 45.67: 515 45.67 - 68.50: 83 68.50 - 91.33: 16 91.33 - 114.17: 1 Dihedral angle restraints: 7227 sinusoidal: 2740 harmonic: 4487 Sorted by residual: dihedral pdb=" CA LYS L 93 " pdb=" C LYS L 93 " pdb=" N PRO L 94 " pdb=" CA PRO L 94 " ideal model delta harmonic sigma weight residual 180.00 126.09 53.91 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CB CYS B 374 " pdb=" SG CYS B 374 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual 93.00 -176.68 -90.32 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 13 " pdb=" SG CYS B 13 " pdb=" SG CYS B 435 " pdb=" CB CYS B 435 " ideal model delta sinusoidal sigma weight residual 93.00 -177.93 -89.07 1 1.00e+01 1.00e-02 9.44e+01 ... (remaining 7224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1444 0.057 - 0.113: 325 0.113 - 0.170: 51 0.170 - 0.226: 1 0.226 - 0.283: 2 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CA PRO B 363 " pdb=" N PRO B 363 " pdb=" C PRO B 363 " pdb=" CB PRO B 363 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO B 443 " pdb=" N PRO B 443 " pdb=" C PRO B 443 " pdb=" CB PRO B 443 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ASP A 245 " pdb=" N ASP A 245 " pdb=" C ASP A 245 " pdb=" CB ASP A 245 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 1820 not shown) Planarity restraints: 2139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 93 " 0.073 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO B 94 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 158 " -0.061 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO H 159 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " 0.015 2.00e-02 2.50e+03 2.12e-02 1.13e+01 pdb=" CG TRP H 33 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " 0.004 2.00e-02 2.50e+03 ... (remaining 2136 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 96 2.54 - 3.13: 8515 3.13 - 3.72: 16871 3.72 - 4.31: 23652 4.31 - 4.90: 42143 Nonbonded interactions: 91277 Sorted by model distance: nonbonded pdb="MG MG B1002 " pdb=" O HOH B1101 " model vdw 1.949 2.170 nonbonded pdb="MG MG B1002 " pdb=" O HOH B1102 " model vdw 1.953 2.170 nonbonded pdb=" OD1 ASP B 217 " pdb="CA CA B1001 " model vdw 2.098 3.250 nonbonded pdb=" OD2 ASP B 158 " pdb="CA CA B1001 " model vdw 2.158 3.250 nonbonded pdb=" ND2 ASN B 215 " pdb="CA CA B1001 " model vdw 2.170 3.330 ... (remaining 91272 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.013 1.047 12024 Z= 0.369 Angle : 1.019 79.302 16385 Z= 0.489 Chirality : 0.049 0.283 1823 Planarity : 0.006 0.106 2139 Dihedral : 16.021 114.166 4298 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.31 % Favored : 92.43 % Rotamer: Outliers : 0.55 % Allowed : 20.41 % Favored : 79.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 3.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.21), residues: 1559 helix: -1.36 (0.42), residues: 127 sheet: -0.02 (0.23), residues: 582 loop : -1.52 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 153 TYR 0.019 0.002 TYR H 109 PHE 0.019 0.002 PHE B 308 TRP 0.054 0.002 TRP H 33 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.01286 / 0.37 (12003) covalent geometry : angle 1.01880 / 0.49 (16343) SS BOND : bond 0.00455 / 0.33 ( 21) SS BOND : angle 1.23826 / 0.77 ( 42) hydrogen bonds : bond 0.14939 / 10.21 ( 396) hydrogen bonds : angle 7.14708 / 4.83 ( 1034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.421 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1057 time to fit residues: 15.7285 Evaluate side-chains 100 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 438 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.211911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151661 restraints weight = 43090.728| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 9.34 r_work: 0.3125 rms_B_bonded: 7.48 restraints_weight: 2.0000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12024 Z= 0.138 Angle : 0.610 13.347 16385 Z= 0.314 Chirality : 0.044 0.144 1823 Planarity : 0.005 0.087 2139 Dihedral : 4.600 52.089 1683 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.85 % Rotamer: Outliers : 1.90 % Allowed : 19.38 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 3.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.21), residues: 1559 helix: -0.72 (0.43), residues: 128 sheet: 0.20 (0.23), residues: 578 loop : -1.42 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.017 0.001 TYR H 27 PHE 0.012 0.001 PHE A 19 TRP 0.028 0.001 TRP H 33 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (12003) covalent geometry : angle 0.60953 / 0.31 (16343) SS BOND : bond 0.00351 / 0.22 ( 21) SS BOND : angle 0.85827 / 0.52 ( 42) hydrogen bonds : bond 0.03356 / 2.34 ( 396) hydrogen bonds : angle 5.82058 / 3.90 ( 1034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6871 (mm-30) REVERT: A 248 LEU cc_start: 0.8794 (mt) cc_final: 0.8593 (mm) REVERT: A 288 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8038 (t80) REVERT: B 207 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8754 (p) REVERT: B 233 ASP cc_start: 0.7644 (m-30) cc_final: 0.7401 (m-30) REVERT: H 32 TYR cc_start: 0.8059 (m-80) cc_final: 0.7839 (m-10) REVERT: L 18 LYS cc_start: 0.8344 (tttt) cc_final: 0.8118 (tttt) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 0.1023 time to fit residues: 19.0039 Evaluate side-chains 119 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 25 optimal weight: 0.0470 chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 450 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.211590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153485 restraints weight = 43160.814| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 8.66 r_work: 0.3116 rms_B_bonded: 7.69 restraints_weight: 2.0000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12024 Z= 0.139 Angle : 0.578 13.259 16385 Z= 0.297 Chirality : 0.044 0.150 1823 Planarity : 0.005 0.084 2139 Dihedral : 4.523 52.065 1683 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.28 % Favored : 93.46 % Rotamer: Outliers : 2.61 % Allowed : 18.67 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1559 helix: -0.43 (0.44), residues: 128 sheet: 0.26 (0.23), residues: 573 loop : -1.38 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.015 0.001 TYR H 27 PHE 0.012 0.002 PHE A 19 TRP 0.028 0.001 TRP H 33 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (12003) covalent geometry : angle 0.57740 / 0.30 (16343) SS BOND : bond 0.00317 / 0.21 ( 21) SS BOND : angle 0.75983 / 0.43 ( 42) hydrogen bonds : bond 0.03078 / 2.13 ( 396) hydrogen bonds : angle 5.53470 / 3.70 ( 1034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8093 (t80) REVERT: A 365 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: B 74 SER cc_start: 0.7259 (t) cc_final: 0.6655 (p) REVERT: B 180 MET cc_start: 0.6978 (mmm) cc_final: 0.6644 (mtt) REVERT: B 233 ASP cc_start: 0.7675 (m-30) cc_final: 0.7395 (m-30) REVERT: H 33 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.6809 (m-10) REVERT: H 50 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7765 (t80) REVERT: H 60 TYR cc_start: 0.8737 (m-80) cc_final: 0.8437 (m-80) REVERT: L 18 LYS cc_start: 0.8337 (tttt) cc_final: 0.8109 (tttt) outliers start: 28 outliers final: 16 residues processed: 134 average time/residue: 0.0987 time to fit residues: 19.7685 Evaluate side-chains 127 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN B 15 GLN B 450 ASN ** H 82 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 = 0.4354 r_free = 0.4354 target = 0.211466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148335 restraints weight = 48025.912| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 15.65 r_work: 0.3153 rms_B_bonded: 7.04 restraints_weight: 2.0000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12024 Z= 0.137 Angle : 0.570 13.306 16385 Z= 0.291 Chirality : 0.044 0.155 1823 Planarity : 0.005 0.082 2139 Dihedral : 4.473 51.962 1683 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.02 % Favored : 93.66 % Rotamer: Outliers : 2.53 % Allowed : 18.67 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.96 (0.21), residues: 1559 helix: -0.36 (0.44), residues: 129 sheet: 0.27 (0.23), residues: 575 loop : -1.34 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.016 0.001 TYR H 27 PHE 0.011 0.001 PHE A 19 TRP 0.027 0.001 TRP H 33 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (12003) covalent geometry : angle 0.56876 / 0.29 (16343) SS BOND : bond 0.00311 / 0.21 ( 21) SS BOND : angle 0.92298 / 0.56 ( 42) hydrogen bonds : bond 0.02882 / 2.00 ( 396) hydrogen bonds : angle 5.36466 / 3.59 ( 1034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8090 (t80) REVERT: A 365 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: B 74 SER cc_start: 0.7256 (t) cc_final: 0.6600 (p) REVERT: B 180 MET cc_start: 0.6898 (mmm) cc_final: 0.6603 (mtt) REVERT: B 207 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8711 (p) REVERT: B 233 ASP cc_start: 0.7663 (m-30) cc_final: 0.7388 (m-30) REVERT: H 33 TRP cc_start: 0.6988 (OUTLIER) cc_final: 0.6709 (m-10) REVERT: H 50 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7787 (t80) REVERT: L 18 LYS cc_start: 0.8258 (tttt) cc_final: 0.8036 (tttt) REVERT: L 89 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7755 (pp30) outliers start: 27 outliers final: 20 residues processed: 130 average time/residue: 0.1046 time to fit residues: 20.1745 Evaluate side-chains 129 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 72 optimal weight: 0.0060 chunk 60 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 142 optimal weight: 0.0370 chunk 144 optimal weight: 0.0000 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 105 optimal weight: 0.6980 overall best weight: 0.1476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN B 450 ASN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.217505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160128 restraints weight = 42039.840| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 8.96 r_work: 0.3226 rms_B_bonded: 7.76 restraints_weight: 2.0000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12024 Z= 0.088 Angle : 0.514 11.683 16385 Z= 0.264 Chirality : 0.042 0.141 1823 Planarity : 0.005 0.077 2139 Dihedral : 4.076 48.428 1683 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.92 % Favored : 94.89 % Rotamer: Outliers : 2.22 % Allowed : 19.07 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.68 (0.21), residues: 1559 helix: 0.05 (0.46), residues: 129 sheet: 0.55 (0.23), residues: 544 loop : -1.21 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.013 0.001 TYR H 27 PHE 0.008 0.001 PHE B 455 TRP 0.021 0.001 TRP H 33 HIS 0.003 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (12003) covalent geometry : angle 0.51328 / 0.26 (16343) SS BOND : bond 0.00218 / 0.15 ( 21) SS BOND : angle 0.68293 / 0.42 ( 42) hydrogen bonds : bond 0.02306 / 1.59 ( 396) hydrogen bonds : angle 4.98975 / 3.32 ( 1034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8366 (mt0) cc_final: 0.8032 (mt0) REVERT: A 158 ASN cc_start: 0.6818 (m-40) cc_final: 0.6309 (t0) REVERT: B 90 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7406 (mp) REVERT: B 207 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 233 ASP cc_start: 0.7742 (m-30) cc_final: 0.7517 (m-30) REVERT: H 50 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7625 (t80) REVERT: L 18 LYS cc_start: 0.8361 (tttt) cc_final: 0.8153 (tttt) REVERT: L 89 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7379 (pp30) outliers start: 23 outliers final: 11 residues processed: 133 average time/residue: 0.0865 time to fit residues: 17.2714 Evaluate side-chains 122 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 152 optimal weight: 50.0000 chunk 142 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN B 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.210997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163654 restraints weight = 36455.046| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 4.00 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12024 Z= 0.124 Angle : 0.545 12.356 16385 Z= 0.278 Chirality : 0.044 0.164 1823 Planarity : 0.005 0.077 2139 Dihedral : 4.201 51.041 1683 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.85 % Rotamer: Outliers : 2.45 % Allowed : 18.99 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.74 (0.21), residues: 1559 helix: 0.07 (0.47), residues: 129 sheet: 0.41 (0.23), residues: 557 loop : -1.21 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.038 0.001 TYR H 109 PHE 0.012 0.001 PHE B 248 TRP 0.038 0.001 TRP H 33 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (12003) covalent geometry : angle 0.54470 / 0.28 (16343) SS BOND : bond 0.00270 / 0.19 ( 21) SS BOND : angle 0.69805 / 0.40 ( 42) hydrogen bonds : bond 0.02586 / 1.78 ( 396) hydrogen bonds : angle 5.01292 / 3.35 ( 1034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.419 Fit side-chains REVERT: A 288 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.7789 (t80) REVERT: B 90 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7311 (mp) REVERT: B 207 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8654 (p) outliers start: 26 outliers final: 18 residues processed: 127 average time/residue: 0.1011 time to fit residues: 19.0656 Evaluate side-chains 126 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 158 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 116 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN B 14 GLN ** H 82 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 = 0.4349 r_free = 0.4349 target = 0.210571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151280 restraints weight = 43629.133| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 9.78 r_work: 0.3137 rms_B_bonded: 7.52 restraints_weight: 2.0000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12024 Z= 0.183 Angle : 0.603 13.262 16385 Z= 0.308 Chirality : 0.046 0.171 1823 Planarity : 0.005 0.078 2139 Dihedral : 4.508 52.354 1683 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.73 % Favored : 93.01 % Rotamer: Outliers : 2.22 % Allowed : 19.22 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1559 helix: -0.20 (0.45), residues: 129 sheet: 0.30 (0.23), residues: 575 loop : -1.27 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.038 0.002 TYR H 109 PHE 0.022 0.002 PHE B 455 TRP 0.023 0.002 TRP H 99 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 (12003) covalent geometry : angle 0.60265 / 0.31 (16343) SS BOND : bond 0.00355 / 0.25 ( 21) SS BOND : angle 0.82926 / 0.46 ( 42) hydrogen bonds : bond 0.03043 / 2.11 ( 396) hydrogen bonds : angle 5.20746 / 3.50 ( 1034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.443 Fit side-chains REVERT: A 288 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8083 (t80) REVERT: B 90 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7384 (mp) REVERT: B 180 MET cc_start: 0.7048 (mtt) cc_final: 0.6499 (mtt) REVERT: B 207 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8752 (p) REVERT: L 18 LYS cc_start: 0.8453 (tttt) cc_final: 0.8252 (tttp) outliers start: 23 outliers final: 17 residues processed: 128 average time/residue: 0.0997 time to fit residues: 18.8627 Evaluate side-chains 124 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 158 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.0670 chunk 153 optimal weight: 4.9990 chunk 70 optimal weight: 0.0870 chunk 137 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.213754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153749 restraints weight = 44333.684| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 9.60 r_work: 0.3182 rms_B_bonded: 7.52 restraints_weight: 2.0000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12024 Z= 0.110 Angle : 0.543 12.596 16385 Z= 0.278 Chirality : 0.043 0.153 1823 Planarity : 0.005 0.076 2139 Dihedral : 4.290 50.523 1683 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.44 % Favored : 94.37 % Rotamer: Outliers : 1.90 % Allowed : 19.62 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.74 (0.21), residues: 1559 helix: -0.07 (0.46), residues: 128 sheet: 0.42 (0.23), residues: 562 loop : -1.20 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.027 0.001 TYR H 109 PHE 0.019 0.001 PHE B 455 TRP 0.021 0.001 TRP H 99 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (12003) covalent geometry : angle 0.54245 / 0.28 (16343) SS BOND : bond 0.00253 / 0.17 ( 21) SS BOND : angle 0.66310 / 0.39 ( 42) hydrogen bonds : bond 0.02532 / 1.75 ( 396) hydrogen bonds : angle 5.02309 / 3.35 ( 1034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.512 Fit side-chains REVERT: A 288 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8079 (t80) REVERT: B 90 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7391 (mp) REVERT: B 180 MET cc_start: 0.7120 (mtt) cc_final: 0.6623 (mtt) REVERT: B 207 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8742 (p) REVERT: L 18 LYS cc_start: 0.8460 (tttt) cc_final: 0.8223 (tttp) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.1097 time to fit residues: 19.7457 Evaluate side-chains 119 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 461 ARG Chi-restraints excluded: chain L residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 94 optimal weight: 0.4980 chunk 143 optimal weight: 0.1980 chunk 132 optimal weight: 0.0670 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 88 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.222753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179783 restraints weight = 37380.679| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.90 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4094 r_free = 0.4094 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4094 r_free = 0.4094 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.4094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12024 Z= 0.095 Angle : 0.519 11.714 16385 Z= 0.266 Chirality : 0.043 0.140 1823 Planarity : 0.005 0.075 2139 Dihedral : 4.072 48.974 1683 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.11 % Favored : 94.69 % Rotamer: Outliers : 1.58 % Allowed : 19.94 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.54 (0.21), residues: 1559 helix: 0.18 (0.47), residues: 128 sheet: 0.67 (0.23), residues: 536 loop : -1.13 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.022 0.001 TYR H 109 PHE 0.015 0.001 PHE B 455 TRP 0.016 0.001 TRP H 99 HIS 0.003 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (12003) covalent geometry : angle 0.51906 / 0.27 (16343) SS BOND : bond 0.00228 / 0.15 ( 21) SS BOND : angle 0.65997 / 0.37 ( 42) hydrogen bonds : bond 0.02321 / 1.60 ( 396) hydrogen bonds : angle 4.82820 / 3.21 ( 1034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.436 Fit side-chains REVERT: B 90 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7251 (mp) REVERT: B 180 MET cc_start: 0.7119 (mtt) cc_final: 0.6780 (mtt) REVERT: B 207 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8640 (p) REVERT: B 233 ASP cc_start: 0.7238 (m-30) cc_final: 0.6933 (m-30) outliers start: 15 outliers final: 10 residues processed: 118 average time/residue: 0.0937 time to fit residues: 16.1624 Evaluate side-chains 114 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 46 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 68 optimal weight: 0.0970 chunk 147 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.219513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156132 restraints weight = 44898.106| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 15.71 r_work: 0.3323 rms_B_bonded: 6.05 restraints_weight: 2.0000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12024 Z= 0.126 Angle : 0.550 12.454 16385 Z= 0.282 Chirality : 0.044 0.151 1823 Planarity : 0.005 0.075 2139 Dihedral : 4.208 50.878 1683 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.85 % Rotamer: Outliers : 1.98 % Allowed : 19.54 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1559 helix: 0.14 (0.47), residues: 128 sheet: 0.48 (0.23), residues: 558 loop : -1.15 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.022 0.001 TYR H 109 PHE 0.016 0.001 PHE B 455 TRP 0.019 0.001 TRP H 99 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (12003) covalent geometry : angle 0.54964 / 0.28 (16343) SS BOND : bond 0.00265 / 0.18 ( 21) SS BOND : angle 0.70765 / 0.41 ( 42) hydrogen bonds : bond 0.02550 / 1.76 ( 396) hydrogen bonds : angle 4.87385 / 3.25 ( 1034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.335 Fit side-chains REVERT: B 90 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7298 (mp) REVERT: B 180 MET cc_start: 0.7146 (mtt) cc_final: 0.6672 (mtt) REVERT: B 207 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8706 (p) outliers start: 20 outliers final: 15 residues processed: 118 average time/residue: 0.0896 time to fit residues: 15.6584 Evaluate side-chains 118 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 460 CYS Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain H residue 158 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 110 optimal weight: 0.0020 chunk 123 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 84 optimal weight: 0.0370 chunk 129 optimal weight: 8.9990 chunk 64 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 overall best weight: 0.3466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.222697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159470 restraints weight = 54900.319| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 16.30 r_work: 0.3251 rms_B_bonded: 7.43 restraints_weight: 2.0000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12024 Z= 0.100 Angle : 0.532 11.962 16385 Z= 0.273 Chirality : 0.043 0.143 1823 Planarity : 0.005 0.073 2139 Dihedral : 4.094 49.509 1683 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.92 % Favored : 94.89 % Rotamer: Outliers : 1.74 % Allowed : 19.78 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 2.25 % 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: -0.50 (0.22), residues: 1559 helix: 0.29 (0.47), residues: 128 sheet: 0.69 (0.23), residues: 542 loop : -1.12 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 37 TYR 0.022 0.001 TYR H 109 PHE 0.013 0.001 PHE H 158 TRP 0.018 0.001 TRP H 99 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (12003) covalent geometry : angle 0.52915 / 0.27 (16343) SS BOND : bond 0.00236 / 0.16 ( 21) SS BOND : angle 1.25228 / 0.81 ( 42) hydrogen bonds : bond 0.02365 / 1.63 ( 396) hydrogen bonds : angle 4.80872 / 3.19 ( 1034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.28 seconds wall clock time: 49 minutes 46.18 seconds (2986.18 seconds total)