Starting phenix.real_space_refine on Wed Mar 4 07:14:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qpd_14119/03_2026/7qpd_14119.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qpd_14119/03_2026/7qpd_14119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qpd_14119/03_2026/7qpd_14119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qpd_14119/03_2026/7qpd_14119.map" model { file = "/net/cci-nas-00/data/ceres_data/7qpd_14119/03_2026/7qpd_14119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qpd_14119/03_2026/7qpd_14119.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 7343 2.51 5 N 1989 2.21 5 O 2147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11521 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 803 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "T" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2569 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 304} Chain breaks: 4 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3365 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 435} Chain breaks: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 19, 'ASN:plan1': 6, 'TYR:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 170 Chain: "M" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2110 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 260} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2552 Classifications: {'peptide': 364} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 119} Link IDs: {'PTRANS': 24, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 576 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 27, 'GLU:plan': 23, 'ASN:plan1': 6, 'GLN:plan1': 4, 'TRP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 298 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.58, per 1000 atoms: 0.22 Number of scatterers: 11521 At special positions: 0 Unit cell: (99.75, 136.5, 131.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2147 8.00 N 1989 7.00 C 7343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 71 " distance=2.03 Simple disulfide: pdb=" SG CYS T 95 " - pdb=" SG CYS E 33 " distance=2.03 Simple disulfide: pdb=" SG CYS T 295 " - pdb=" SG CYS T 362 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 382 " - pdb=" SG CYS E 385 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 164 " distance=2.03 Simple disulfide: pdb=" SG CYS M 203 " - pdb=" SG CYS M 259 " distance=2.04 Simple disulfide: pdb=" SG CYS C 88 " - pdb=" SG CYS C 120 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN D 5 " - " MAN D 6 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " GLC D 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 1 " - " ASN T 233 " " NAG D 1 " - " ASN M 86 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 425.3 milliseconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 27 sheets defined 23.9% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'T' and resid 41 through 44 Processing helix chain 'T' and resid 53 through 61 removed outlier: 3.629A pdb=" N ALA T 57 " --> pdb=" O GLY T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 90 removed outlier: 4.387A pdb=" N GLY T 88 " --> pdb=" O TRP T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 100 No H-bonds generated for 'chain 'T' and resid 98 through 100' Processing helix chain 'T' and resid 242 through 246 Processing helix chain 'E' and resid 7 through 9 No H-bonds generated for 'chain 'E' and resid 7 through 9' Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.929A pdb=" N SER E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 50 removed outlier: 3.787A pdb=" N LYS E 37 " --> pdb=" O CYS E 33 " (cutoff:3.500A) Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 64 through 72 removed outlier: 4.257A pdb=" N CYS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 removed outlier: 3.556A pdb=" N GLY E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 141 through 154 Processing helix chain 'E' and resid 165 through 171 Processing helix chain 'E' and resid 184 through 188 removed outlier: 3.949A pdb=" N THR E 188 " --> pdb=" O SER E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.525A pdb=" N ILE E 231 " --> pdb=" O ASN E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 270 removed outlier: 8.156A pdb=" N LYS E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 removed outlier: 3.935A pdb=" N SER E 288 " --> pdb=" O SER E 284 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 335 Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 382 through 399 Proline residue: E 390 - end of helix Processing helix chain 'E' and resid 400 through 402 No H-bonds generated for 'chain 'E' and resid 400 through 402' Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'M' and resid 49 through 54 removed outlier: 4.034A pdb=" N GLN M 54 " --> pdb=" O PRO M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 3.734A pdb=" N VAL M 76 " --> pdb=" O GLN M 72 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 151 removed outlier: 3.541A pdb=" N ALA M 150 " --> pdb=" O LYS M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 162 removed outlier: 3.521A pdb=" N ALA M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 175 Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.818A pdb=" N ARG C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 285 through 289 removed outlier: 4.172A pdb=" N TYR C 289 " --> pdb=" O PRO C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 369 removed outlier: 4.446A pdb=" N VAL C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9 removed outlier: 3.646A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 45 removed outlier: 3.632A pdb=" N GLU B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 9 through 10 Processing sheet with id=AA5, first strand: chain 'T' and resid 46 through 49 removed outlier: 3.600A pdb=" N ALA T 135 " --> pdb=" O SER T 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL T 137 " --> pdb=" O HIS T 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 95 through 96 Processing sheet with id=AA7, first strand: chain 'T' and resid 139 through 142 Processing sheet with id=AA8, first strand: chain 'T' and resid 149 through 151 removed outlier: 6.256A pdb=" N VAL T 150 " --> pdb=" O TYR T 269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY T 247 " --> pdb=" O LEU T 266 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR T 248 " --> pdb=" O GLN T 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU T 198 " --> pdb=" O TRP T 186 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG T 188 " --> pdb=" O LEU T 196 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU T 196 " --> pdb=" O ARG T 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 149 through 151 removed outlier: 6.256A pdb=" N VAL T 150 " --> pdb=" O TYR T 269 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY T 247 " --> pdb=" O LEU T 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 156 through 158 Processing sheet with id=AB2, first strand: chain 'T' and resid 274 through 277 Processing sheet with id=AB3, first strand: chain 'T' and resid 321 through 322 Processing sheet with id=AB4, first strand: chain 'T' and resid 334 through 335 removed outlier: 4.470A pdb=" N TRP M 244 " --> pdb=" O VAL M 231 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR M 233 " --> pdb=" O GLN M 242 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN M 242 " --> pdb=" O THR M 233 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE M 241 " --> pdb=" O GLY M 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 4 through 5 removed outlier: 6.090A pdb=" N LEU E 4 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASP E 60 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE E 81 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.761A pdb=" N GLY E 178 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 276 through 279 removed outlier: 6.140A pdb=" N ALA E 239 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 355 through 357 removed outlier: 4.271A pdb=" N ASP E 411 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP E 372 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA E 408 " --> pdb=" O ASP E 372 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU E 374 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N MET E 410 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU E 376 " --> pdb=" O MET E 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 31 through 37 removed outlier: 5.308A pdb=" N GLN M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL M 28 " --> pdb=" O GLN M 32 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL M 34 " --> pdb=" O GLY M 26 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG M 114 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR M 118 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 222 through 223 Processing sheet with id=AC2, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AC3, first strand: chain 'C' and resid 6 through 8 removed outlier: 4.197A pdb=" N PHE C 313 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLN C 77 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 315 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 75 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR C 165 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER C 176 " --> pdb=" O TYR C 165 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 167 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 21 through 22 removed outlier: 9.904A pdb=" N SER C 63 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N GLY C 298 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N GLU C 65 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 296 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE C 96 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU C 297 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 94 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 113 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.608A pdb=" N ARG C 56 " --> pdb=" O GLN C 303 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 303 " --> pdb=" O ARG C 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.612A pdb=" N ASP C 118 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS C 126 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 190 through 192 Processing sheet with id=AC8, first strand: chain 'C' and resid 207 through 208 Processing sheet with id=AC9, first strand: chain 'C' and resid 224 through 226 467 hydrogen bonds defined for protein. 1230 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: 1.99 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3754 1.34 - 1.46: 2826 1.46 - 1.59: 5195 1.59 - 1.71: 0 1.71 - 1.83: 63 Bond restraints: 11838 Sorted by residual: bond pdb=" N VAL C 174 " pdb=" CA VAL C 174 " ideal model delta sigma weight residual 1.456 1.496 -0.039 9.50e-03 1.11e+04 1.70e+01 bond pdb=" N PRO M 50 " pdb=" CD PRO M 50 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N VAL C 93 " pdb=" CA VAL C 93 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N ILE C 86 " pdb=" CA ILE C 86 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.83e+00 bond pdb=" N GLU B 74 " pdb=" CA GLU B 74 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.12e-02 7.97e+03 9.26e+00 ... (remaining 11833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 15349 1.77 - 3.53: 728 3.53 - 5.30: 74 5.30 - 7.07: 20 7.07 - 8.83: 2 Bond angle restraints: 16173 Sorted by residual: angle pdb=" N ASP M 29 " pdb=" CA ASP M 29 " pdb=" C ASP M 29 " ideal model delta sigma weight residual 108.00 100.75 7.25 1.48e+00 4.57e-01 2.40e+01 angle pdb=" N VAL M 28 " pdb=" CA VAL M 28 " pdb=" C VAL M 28 " ideal model delta sigma weight residual 107.80 100.82 6.98 1.45e+00 4.76e-01 2.31e+01 angle pdb=" N ASP C 87 " pdb=" CA ASP C 87 " pdb=" C ASP C 87 " ideal model delta sigma weight residual 113.12 107.95 5.17 1.25e+00 6.40e-01 1.71e+01 angle pdb=" N LYS T 193 " pdb=" CA LYS T 193 " pdb=" C LYS T 193 " ideal model delta sigma weight residual 112.12 106.59 5.53 1.34e+00 5.57e-01 1.70e+01 angle pdb=" N VAL C 174 " pdb=" CA VAL C 174 " pdb=" C VAL C 174 " ideal model delta sigma weight residual 113.53 109.60 3.93 9.80e-01 1.04e+00 1.61e+01 ... (remaining 16168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 6816 21.64 - 43.27: 256 43.27 - 64.91: 29 64.91 - 86.55: 17 86.55 - 108.18: 9 Dihedral angle restraints: 7127 sinusoidal: 2656 harmonic: 4471 Sorted by residual: dihedral pdb=" CB CYS E 61 " pdb=" SG CYS E 61 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 178.31 -85.31 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA ILE E 304 " pdb=" C ILE E 304 " pdb=" N ARG E 305 " pdb=" CA ARG E 305 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" O4 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C5 BMA A 3 " pdb=" O5 BMA A 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.47 108.18 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 7124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1456 0.059 - 0.118: 286 0.118 - 0.177: 40 0.177 - 0.236: 7 0.236 - 0.295: 4 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CA ILE C 113 " pdb=" N ILE C 113 " pdb=" C ILE C 113 " pdb=" CB ILE C 113 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1790 not shown) Planarity restraints: 2121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR M 27 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C TYR M 27 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR M 27 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL M 28 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 60 " 0.015 2.00e-02 2.50e+03 1.43e-02 5.09e+00 pdb=" CG TRP M 60 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP M 60 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP M 60 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP M 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 60 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 60 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 60 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP M 60 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP M 29 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C ASP M 29 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP M 29 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP M 30 " 0.013 2.00e-02 2.50e+03 ... (remaining 2118 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1591 2.76 - 3.29: 10755 3.29 - 3.83: 18482 3.83 - 4.36: 21025 4.36 - 4.90: 36894 Nonbonded interactions: 88747 Sorted by model distance: nonbonded pdb=" OH TYR B 10 " pdb=" O PRO M 235 " model vdw 2.225 3.040 nonbonded pdb=" O GLN T 245 " pdb=" OH TYR T 249 " model vdw 2.237 3.040 nonbonded pdb=" N GLY C 30 " pdb=" O PHE C 57 " model vdw 2.323 3.120 nonbonded pdb=" OE2 GLU E 286 " pdb=" NH2 ARG E 305 " model vdw 2.358 3.120 nonbonded pdb=" NH1 ARG B 45 " pdb=" O ILE B 46 " model vdw 2.388 3.120 ... (remaining 88742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.050 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11857 Z= 0.318 Angle : 0.814 8.835 16221 Z= 0.493 Chirality : 0.051 0.295 1793 Planarity : 0.005 0.050 2119 Dihedral : 12.543 108.182 4218 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 0.09 % Allowed : 0.94 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.22), residues: 1522 helix: 1.11 (0.30), residues: 297 sheet: -1.59 (0.24), residues: 416 loop : -1.03 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 349 TYR 0.012 0.001 TYR B 63 PHE 0.031 0.002 PHE C 325 TRP 0.038 0.002 TRP M 60 HIS 0.004 0.001 HIS T 345 Details of bonding type rmsd covalent geometry : bond 0.00481 (11838) covalent geometry : angle 0.80851 (16173) SS BOND : bond 0.00420 ( 9) SS BOND : angle 1.12602 ( 18) hydrogen bonds : bond 0.14914 ( 462) hydrogen bonds : angle 7.00347 ( 1230) link_ALPHA1-2 : bond 0.00186 ( 2) link_ALPHA1-2 : angle 1.97868 ( 6) link_ALPHA1-3 : bond 0.00428 ( 2) link_ALPHA1-3 : angle 2.32884 ( 6) link_BETA1-4 : bond 0.00139 ( 4) link_BETA1-4 : angle 2.30541 ( 12) link_NAG-ASN : bond 0.00583 ( 2) link_NAG-ASN : angle 2.00095 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.6630 (mt) cc_final: 0.6338 (mt) REVERT: T 87 SER cc_start: 0.8633 (p) cc_final: 0.8368 (t) REVERT: C 92 TYR cc_start: 0.6936 (p90) cc_final: 0.6670 (p90) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.1312 time to fit residues: 38.6105 Evaluate side-chains 122 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 28 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 242 GLN M 72 GLN ** M 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 173 GLN ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.150103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115634 restraints weight = 19642.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111582 restraints weight = 26851.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107295 restraints weight = 19944.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106796 restraints weight = 21954.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107223 restraints weight = 19378.185| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11857 Z= 0.212 Angle : 0.710 8.952 16221 Z= 0.355 Chirality : 0.046 0.318 1793 Planarity : 0.005 0.047 2119 Dihedral : 8.604 73.814 1849 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 1.98 % Allowed : 8.87 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1522 helix: 1.36 (0.29), residues: 302 sheet: -1.39 (0.25), residues: 428 loop : -0.98 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 65 TYR 0.025 0.002 TYR B 67 PHE 0.023 0.002 PHE T 236 TRP 0.012 0.002 TRP M 244 HIS 0.011 0.002 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00485 (11838) covalent geometry : angle 0.69894 (16173) SS BOND : bond 0.00638 ( 9) SS BOND : angle 1.99838 ( 18) hydrogen bonds : bond 0.04260 ( 462) hydrogen bonds : angle 5.60720 ( 1230) link_ALPHA1-2 : bond 0.00674 ( 2) link_ALPHA1-2 : angle 1.70697 ( 6) link_ALPHA1-3 : bond 0.00185 ( 2) link_ALPHA1-3 : angle 2.21072 ( 6) link_BETA1-4 : bond 0.00239 ( 4) link_BETA1-4 : angle 2.92288 ( 12) link_NAG-ASN : bond 0.00252 ( 2) link_NAG-ASN : angle 2.76667 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.7304 (mt) cc_final: 0.6911 (mt) REVERT: T 87 SER cc_start: 0.8620 (p) cc_final: 0.8369 (t) REVERT: C 321 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6808 (t80) REVERT: C 349 ARG cc_start: 0.8703 (tmm-80) cc_final: 0.8301 (tmm-80) outliers start: 21 outliers final: 10 residues processed: 142 average time/residue: 0.0969 time to fit residues: 20.3547 Evaluate side-chains 125 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 277 MET Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain M residue 72 GLN Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 321 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 17 optimal weight: 0.0010 chunk 7 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 82 optimal weight: 0.0030 chunk 29 optimal weight: 0.0170 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS C 173 GLN ** C 303 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 = 0.4129 r_free = 0.4129 target = 0.153634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120604 restraints weight = 19674.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117115 restraints weight = 25449.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.112584 restraints weight = 16324.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112171 restraints weight = 21226.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112123 restraints weight = 19151.628| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11857 Z= 0.117 Angle : 0.634 10.381 16221 Z= 0.313 Chirality : 0.044 0.254 1793 Planarity : 0.005 0.047 2119 Dihedral : 7.423 61.900 1848 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 1.60 % Allowed : 11.32 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.79 (0.22), residues: 1522 helix: 1.40 (0.30), residues: 308 sheet: -1.11 (0.25), residues: 428 loop : -0.90 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 19 TYR 0.026 0.001 TYR B 67 PHE 0.023 0.001 PHE C 115 TRP 0.019 0.001 TRP T 230 HIS 0.006 0.001 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00255 (11838) covalent geometry : angle 0.62526 (16173) SS BOND : bond 0.01080 ( 9) SS BOND : angle 1.50754 ( 18) hydrogen bonds : bond 0.03704 ( 462) hydrogen bonds : angle 5.27969 ( 1230) link_ALPHA1-2 : bond 0.00815 ( 2) link_ALPHA1-2 : angle 1.73429 ( 6) link_ALPHA1-3 : bond 0.00441 ( 2) link_ALPHA1-3 : angle 1.91573 ( 6) link_BETA1-4 : bond 0.00667 ( 4) link_BETA1-4 : angle 2.68926 ( 12) link_NAG-ASN : bond 0.00078 ( 2) link_NAG-ASN : angle 1.81619 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.7411 (mt) cc_final: 0.6989 (mt) REVERT: T 87 SER cc_start: 0.8663 (p) cc_final: 0.8361 (t) REVERT: C 254 TYR cc_start: 0.5179 (t80) cc_final: 0.4045 (t80) outliers start: 17 outliers final: 9 residues processed: 142 average time/residue: 0.0981 time to fit residues: 20.4451 Evaluate side-chains 130 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN M 192 HIS C 303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.150453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.115893 restraints weight = 19551.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111267 restraints weight = 26336.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109267 restraints weight = 19562.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108476 restraints weight = 19314.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108966 restraints weight = 19825.548| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11857 Z= 0.159 Angle : 0.649 13.985 16221 Z= 0.315 Chirality : 0.044 0.300 1793 Planarity : 0.005 0.046 2119 Dihedral : 6.492 57.020 1848 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 2.26 % Allowed : 13.58 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.22), residues: 1522 helix: 1.61 (0.29), residues: 307 sheet: -1.04 (0.25), residues: 434 loop : -0.86 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.026 0.002 TYR B 67 PHE 0.019 0.002 PHE T 236 TRP 0.029 0.001 TRP M 204 HIS 0.005 0.001 HIS M 192 Details of bonding type rmsd covalent geometry : bond 0.00365 (11838) covalent geometry : angle 0.63806 (16173) SS BOND : bond 0.00567 ( 9) SS BOND : angle 2.16429 ( 18) hydrogen bonds : bond 0.03473 ( 462) hydrogen bonds : angle 5.08974 ( 1230) link_ALPHA1-2 : bond 0.00627 ( 2) link_ALPHA1-2 : angle 1.66847 ( 6) link_ALPHA1-3 : bond 0.00414 ( 2) link_ALPHA1-3 : angle 1.75884 ( 6) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 2.67996 ( 12) link_NAG-ASN : bond 0.00300 ( 2) link_NAG-ASN : angle 2.49698 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.7505 (mt) cc_final: 0.7094 (mt) REVERT: T 50 ASP cc_start: 0.7903 (t0) cc_final: 0.7620 (t0) REVERT: T 87 SER cc_start: 0.8579 (p) cc_final: 0.8264 (t) REVERT: T 165 MET cc_start: 0.6925 (tpp) cc_final: 0.6466 (tpp) REVERT: E 24 MET cc_start: 0.4241 (tpt) cc_final: 0.3937 (tpp) REVERT: C 254 TYR cc_start: 0.4812 (t80) cc_final: 0.3914 (t80) outliers start: 24 outliers final: 12 residues processed: 148 average time/residue: 0.0913 time to fit residues: 20.3979 Evaluate side-chains 131 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 303 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 326 GLN C 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.112331 restraints weight = 19490.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110594 restraints weight = 27136.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107816 restraints weight = 22714.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107631 restraints weight = 24894.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108067 restraints weight = 18919.158| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11857 Z= 0.219 Angle : 0.689 16.152 16221 Z= 0.342 Chirality : 0.044 0.321 1793 Planarity : 0.005 0.045 2119 Dihedral : 6.508 58.052 1848 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 2.64 % Allowed : 14.62 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.76 (0.22), residues: 1522 helix: 1.47 (0.29), residues: 312 sheet: -0.97 (0.25), residues: 439 loop : -0.99 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.028 0.002 TYR B 67 PHE 0.025 0.002 PHE B 30 TRP 0.012 0.001 TRP M 244 HIS 0.005 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00498 (11838) covalent geometry : angle 0.67490 (16173) SS BOND : bond 0.00543 ( 9) SS BOND : angle 2.97962 ( 18) hydrogen bonds : bond 0.03615 ( 462) hydrogen bonds : angle 5.13698 ( 1230) link_ALPHA1-2 : bond 0.00482 ( 2) link_ALPHA1-2 : angle 1.69893 ( 6) link_ALPHA1-3 : bond 0.00387 ( 2) link_ALPHA1-3 : angle 1.68022 ( 6) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 2.60704 ( 12) link_NAG-ASN : bond 0.00440 ( 2) link_NAG-ASN : angle 2.81873 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: B 17 ASN cc_start: 0.7463 (t0) cc_final: 0.7193 (m-40) REVERT: B 42 ASN cc_start: 0.7577 (t0) cc_final: 0.7323 (t0) REVERT: T 40 LEU cc_start: 0.7568 (mt) cc_final: 0.7128 (mt) REVERT: T 50 ASP cc_start: 0.7930 (t0) cc_final: 0.7661 (t0) REVERT: T 87 SER cc_start: 0.8670 (p) cc_final: 0.8356 (t) REVERT: T 90 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8277 (p) REVERT: C 254 TYR cc_start: 0.4231 (t80) cc_final: 0.3413 (t80) REVERT: C 349 ARG cc_start: 0.8543 (tmm-80) cc_final: 0.8189 (tmm-80) outliers start: 28 outliers final: 16 residues processed: 146 average time/residue: 0.0936 time to fit residues: 20.0753 Evaluate side-chains 133 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 56 GLN Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS T 326 GLN T 345 HIS ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.147207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111087 restraints weight = 19601.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110281 restraints weight = 26635.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106773 restraints weight = 17549.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.105824 restraints weight = 19589.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106085 restraints weight = 18012.281| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11857 Z= 0.226 Angle : 0.690 11.708 16221 Z= 0.343 Chirality : 0.044 0.321 1793 Planarity : 0.005 0.045 2119 Dihedral : 6.507 58.458 1848 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 2.36 % Allowed : 15.66 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.85 (0.22), residues: 1522 helix: 1.44 (0.29), residues: 312 sheet: -1.02 (0.26), residues: 408 loop : -1.11 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 97 TYR 0.028 0.002 TYR B 67 PHE 0.026 0.002 PHE B 30 TRP 0.012 0.001 TRP M 244 HIS 0.005 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00514 (11838) covalent geometry : angle 0.67889 (16173) SS BOND : bond 0.00601 ( 9) SS BOND : angle 2.38476 ( 18) hydrogen bonds : bond 0.03661 ( 462) hydrogen bonds : angle 5.19175 ( 1230) link_ALPHA1-2 : bond 0.00462 ( 2) link_ALPHA1-2 : angle 1.79229 ( 6) link_ALPHA1-3 : bond 0.00509 ( 2) link_ALPHA1-3 : angle 1.66055 ( 6) link_BETA1-4 : bond 0.00240 ( 4) link_BETA1-4 : angle 2.61814 ( 12) link_NAG-ASN : bond 0.00503 ( 2) link_NAG-ASN : angle 3.02147 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7828 (t0) cc_final: 0.7423 (t0) REVERT: T 40 LEU cc_start: 0.7556 (mt) cc_final: 0.7167 (mt) REVERT: T 50 ASP cc_start: 0.7971 (t0) cc_final: 0.7714 (t0) REVERT: T 87 SER cc_start: 0.8673 (p) cc_final: 0.8356 (t) REVERT: T 326 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7481 (pp30) REVERT: E 160 PHE cc_start: 0.6908 (m-80) cc_final: 0.6245 (m-80) REVERT: C 92 TYR cc_start: 0.6387 (p90) cc_final: 0.6029 (p90) REVERT: C 254 TYR cc_start: 0.4481 (t80) cc_final: 0.3693 (t80) REVERT: C 349 ARG cc_start: 0.8604 (tmm-80) cc_final: 0.8220 (tmm-80) outliers start: 25 outliers final: 19 residues processed: 137 average time/residue: 0.0918 time to fit residues: 18.8827 Evaluate side-chains 139 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 56 GLN Chi-restraints excluded: chain T residue 100 ASP Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 326 GLN Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 321 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 142 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 147 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.148503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114539 restraints weight = 19803.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112097 restraints weight = 27379.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107189 restraints weight = 17702.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106488 restraints weight = 21571.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107268 restraints weight = 19253.212| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11857 Z= 0.167 Angle : 0.656 12.679 16221 Z= 0.324 Chirality : 0.043 0.299 1793 Planarity : 0.005 0.048 2119 Dihedral : 6.246 58.987 1848 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 1.60 % Allowed : 16.13 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.79 (0.22), residues: 1522 helix: 1.48 (0.29), residues: 312 sheet: -0.92 (0.26), residues: 397 loop : -1.11 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.026 0.001 TYR B 67 PHE 0.023 0.002 PHE C 115 TRP 0.013 0.001 TRP C 302 HIS 0.004 0.001 HIS T 345 Details of bonding type rmsd covalent geometry : bond 0.00380 (11838) covalent geometry : angle 0.64663 (16173) SS BOND : bond 0.00519 ( 9) SS BOND : angle 1.84333 ( 18) hydrogen bonds : bond 0.03508 ( 462) hydrogen bonds : angle 5.09731 ( 1230) link_ALPHA1-2 : bond 0.00470 ( 2) link_ALPHA1-2 : angle 1.77272 ( 6) link_ALPHA1-3 : bond 0.00527 ( 2) link_ALPHA1-3 : angle 1.55402 ( 6) link_BETA1-4 : bond 0.00275 ( 4) link_BETA1-4 : angle 2.50701 ( 12) link_NAG-ASN : bond 0.00394 ( 2) link_NAG-ASN : angle 2.68475 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7750 (t0) cc_final: 0.7366 (t0) REVERT: T 40 LEU cc_start: 0.7534 (mt) cc_final: 0.7164 (mt) REVERT: T 50 ASP cc_start: 0.7926 (t0) cc_final: 0.7651 (t0) REVERT: T 87 SER cc_start: 0.8697 (p) cc_final: 0.8402 (t) REVERT: E 160 PHE cc_start: 0.7042 (m-80) cc_final: 0.6415 (m-80) REVERT: C 254 TYR cc_start: 0.4624 (t80) cc_final: 0.3874 (t80) REVERT: C 349 ARG cc_start: 0.8672 (tmm-80) cc_final: 0.8260 (tmm-80) outliers start: 17 outliers final: 16 residues processed: 133 average time/residue: 0.0955 time to fit residues: 19.1216 Evaluate side-chains 129 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 56 GLN Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 321 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.149474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.116094 restraints weight = 19523.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111265 restraints weight = 24691.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106158 restraints weight = 18590.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106083 restraints weight = 22786.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106176 restraints weight = 20820.658| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11857 Z= 0.147 Angle : 0.658 13.460 16221 Z= 0.322 Chirality : 0.043 0.288 1793 Planarity : 0.005 0.050 2119 Dihedral : 5.925 58.966 1848 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 1.79 % Allowed : 16.51 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.73 (0.22), residues: 1522 helix: 1.59 (0.29), residues: 312 sheet: -0.91 (0.26), residues: 410 loop : -1.06 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 19 TYR 0.024 0.001 TYR B 67 PHE 0.025 0.002 PHE C 115 TRP 0.015 0.001 TRP M 204 HIS 0.004 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00338 (11838) covalent geometry : angle 0.64970 (16173) SS BOND : bond 0.00477 ( 9) SS BOND : angle 1.67472 ( 18) hydrogen bonds : bond 0.03362 ( 462) hydrogen bonds : angle 4.97832 ( 1230) link_ALPHA1-2 : bond 0.00528 ( 2) link_ALPHA1-2 : angle 1.67913 ( 6) link_ALPHA1-3 : bond 0.00572 ( 2) link_ALPHA1-3 : angle 1.54289 ( 6) link_BETA1-4 : bond 0.00269 ( 4) link_BETA1-4 : angle 2.46551 ( 12) link_NAG-ASN : bond 0.00333 ( 2) link_NAG-ASN : angle 2.47410 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7808 (t0) cc_final: 0.7453 (t0) REVERT: T 40 LEU cc_start: 0.7513 (mt) cc_final: 0.7116 (mt) REVERT: T 50 ASP cc_start: 0.7865 (t0) cc_final: 0.7603 (t0) REVERT: T 87 SER cc_start: 0.8636 (p) cc_final: 0.8337 (t) REVERT: E 160 PHE cc_start: 0.7492 (m-80) cc_final: 0.6928 (m-80) REVERT: C 254 TYR cc_start: 0.5210 (t80) cc_final: 0.4490 (t80) REVERT: C 349 ARG cc_start: 0.8778 (tmm-80) cc_final: 0.8295 (tmm-80) outliers start: 19 outliers final: 16 residues processed: 130 average time/residue: 0.0932 time to fit residues: 18.0657 Evaluate side-chains 131 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 56 GLN Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 303 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 73 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 3 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.149952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116923 restraints weight = 19728.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107309 restraints weight = 24769.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107052 restraints weight = 22200.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107343 restraints weight = 19669.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107300 restraints weight = 17653.202| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11857 Z= 0.132 Angle : 0.640 13.170 16221 Z= 0.314 Chirality : 0.043 0.282 1793 Planarity : 0.005 0.052 2119 Dihedral : 5.689 58.865 1848 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 1.70 % Allowed : 16.51 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.67 (0.22), residues: 1522 helix: 1.70 (0.29), residues: 312 sheet: -0.91 (0.26), residues: 410 loop : -1.04 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.024 0.001 TYR B 67 PHE 0.017 0.001 PHE T 236 TRP 0.020 0.001 TRP C 302 HIS 0.004 0.001 HIS M 191 Details of bonding type rmsd covalent geometry : bond 0.00308 (11838) covalent geometry : angle 0.63285 (16173) SS BOND : bond 0.00440 ( 9) SS BOND : angle 1.50792 ( 18) hydrogen bonds : bond 0.03300 ( 462) hydrogen bonds : angle 4.88747 ( 1230) link_ALPHA1-2 : bond 0.00510 ( 2) link_ALPHA1-2 : angle 1.65650 ( 6) link_ALPHA1-3 : bond 0.00495 ( 2) link_ALPHA1-3 : angle 1.62527 ( 6) link_BETA1-4 : bond 0.00270 ( 4) link_BETA1-4 : angle 2.40750 ( 12) link_NAG-ASN : bond 0.00308 ( 2) link_NAG-ASN : angle 2.31403 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7718 (t0) cc_final: 0.7359 (t0) REVERT: T 40 LEU cc_start: 0.7494 (mt) cc_final: 0.7085 (mt) REVERT: T 50 ASP cc_start: 0.7746 (t0) cc_final: 0.7473 (t0) REVERT: T 87 SER cc_start: 0.8559 (p) cc_final: 0.8262 (t) REVERT: E 160 PHE cc_start: 0.7536 (m-80) cc_final: 0.6986 (m-80) REVERT: C 254 TYR cc_start: 0.5294 (t80) cc_final: 0.4570 (t80) REVERT: C 339 GLN cc_start: 0.8942 (pp30) cc_final: 0.8707 (pp30) REVERT: C 349 ARG cc_start: 0.8735 (tmm-80) cc_final: 0.8263 (tmm-80) outliers start: 18 outliers final: 18 residues processed: 128 average time/residue: 0.0919 time to fit residues: 17.6024 Evaluate side-chains 135 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 56 GLN Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 303 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.148721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.115626 restraints weight = 19825.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107149 restraints weight = 26527.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105533 restraints weight = 21853.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105380 restraints weight = 21443.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105893 restraints weight = 18273.749| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11857 Z= 0.169 Angle : 0.670 13.472 16221 Z= 0.327 Chirality : 0.043 0.298 1793 Planarity : 0.005 0.051 2119 Dihedral : 5.610 58.419 1848 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 1.98 % Allowed : 16.51 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.67 (0.22), residues: 1522 helix: 1.74 (0.29), residues: 312 sheet: -0.91 (0.26), residues: 396 loop : -1.06 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 160 TYR 0.029 0.002 TYR B 67 PHE 0.019 0.002 PHE B 30 TRP 0.021 0.001 TRP C 302 HIS 0.005 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00392 (11838) covalent geometry : angle 0.66238 (16173) SS BOND : bond 0.00498 ( 9) SS BOND : angle 1.59803 ( 18) hydrogen bonds : bond 0.03330 ( 462) hydrogen bonds : angle 4.90406 ( 1230) link_ALPHA1-2 : bond 0.00458 ( 2) link_ALPHA1-2 : angle 1.63586 ( 6) link_ALPHA1-3 : bond 0.00402 ( 2) link_ALPHA1-3 : angle 1.58838 ( 6) link_BETA1-4 : bond 0.00226 ( 4) link_BETA1-4 : angle 2.48657 ( 12) link_NAG-ASN : bond 0.00417 ( 2) link_NAG-ASN : angle 2.57127 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7752 (t0) cc_final: 0.7398 (t0) REVERT: T 40 LEU cc_start: 0.7539 (mt) cc_final: 0.7140 (mt) REVERT: T 50 ASP cc_start: 0.7819 (t0) cc_final: 0.7573 (t0) REVERT: T 87 SER cc_start: 0.8620 (p) cc_final: 0.8315 (t) REVERT: E 160 PHE cc_start: 0.7481 (m-80) cc_final: 0.7013 (m-80) REVERT: C 254 TYR cc_start: 0.5201 (t80) cc_final: 0.4521 (t80) REVERT: C 339 GLN cc_start: 0.8955 (pp30) cc_final: 0.8747 (pp30) REVERT: C 349 ARG cc_start: 0.8694 (tmm-80) cc_final: 0.8202 (tmm-80) outliers start: 21 outliers final: 19 residues processed: 130 average time/residue: 0.0849 time to fit residues: 16.9755 Evaluate side-chains 138 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain T residue 56 GLN Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 150 VAL Chi-restraints excluded: chain T residue 227 TRP Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 151 HIS Chi-restraints excluded: chain M residue 189 MET Chi-restraints excluded: chain M residue 259 CYS Chi-restraints excluded: chain M residue 261 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 303 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 115 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.149424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.116532 restraints weight = 19800.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109162 restraints weight = 27606.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107408 restraints weight = 21413.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.106790 restraints weight = 23018.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.106854 restraints weight = 21243.808| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11857 Z= 0.150 Angle : 0.653 13.326 16221 Z= 0.318 Chirality : 0.043 0.291 1793 Planarity : 0.005 0.051 2119 Dihedral : 5.483 58.695 1848 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 1.79 % Allowed : 16.60 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.22), residues: 1522 helix: 1.75 (0.29), residues: 312 sheet: -0.91 (0.26), residues: 409 loop : -1.04 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 19 TYR 0.029 0.001 TYR B 67 PHE 0.017 0.001 PHE T 236 TRP 0.051 0.002 TRP M 51 HIS 0.004 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00347 (11838) covalent geometry : angle 0.64276 (16173) SS BOND : bond 0.00609 ( 9) SS BOND : angle 2.22319 ( 18) hydrogen bonds : bond 0.03307 ( 462) hydrogen bonds : angle 4.87925 ( 1230) link_ALPHA1-2 : bond 0.00521 ( 2) link_ALPHA1-2 : angle 1.57252 ( 6) link_ALPHA1-3 : bond 0.00399 ( 2) link_ALPHA1-3 : angle 1.56373 ( 6) link_BETA1-4 : bond 0.00274 ( 4) link_BETA1-4 : angle 2.44257 ( 12) link_NAG-ASN : bond 0.00364 ( 2) link_NAG-ASN : angle 2.45181 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.52 seconds wall clock time: 34 minutes 53.39 seconds (2093.39 seconds total)