Starting phenix.real_space_refine on Tue Jun 10 14:50:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qpd_14119/06_2025/7qpd_14119.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qpd_14119/06_2025/7qpd_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_14119/06_2025/7qpd_14119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qpd_14119/06_2025/7qpd_14119.map" model { file = "/net/cci-nas-00/data/ceres_data/7qpd_14119/06_2025/7qpd_14119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qpd_14119/06_2025/7qpd_14119.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 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: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} 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: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 27, 'GLU:plan': 23, 'ARG: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: 7.76, per 1000 atoms: 0.67 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: 3.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.70 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: 3.93 Time building geometry restraints manager: 3.52 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: 3.240 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.180 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- 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 : 9.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.038 0.002 TRP M 60 HIS 0.004 0.001 HIS T 345 PHE 0.031 0.002 PHE C 325 TYR 0.012 0.001 TYR B 63 ARG 0.009 0.001 ARG C 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 2) link_NAG-ASN : angle 2.00095 ( 6) link_BETA1-4 : bond 0.00139 ( 4) link_BETA1-4 : angle 2.30541 ( 12) 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) hydrogen bonds : bond 0.14914 ( 462) hydrogen bonds : angle 7.00347 ( 1230) SS BOND : bond 0.00420 ( 9) SS BOND : angle 1.12602 ( 18) covalent geometry : bond 0.00481 (11838) covalent geometry : angle 0.80851 (16173) *********************** 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 : 1.372 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: 0.6629 (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: 0.6668 (p90) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.2940 time to fit residues: 86.2825 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 : 1.179 ------------------------------------------------------------------------------- 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 127 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 242 GLN M 72 GLN M 192 HIS C 137 ASN C 173 GLN ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.152173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.118434 restraints weight = 19455.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110535 restraints weight = 26015.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107176 restraints weight = 21037.166| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11857 Z= 0.156 Angle : 0.676 9.171 16221 Z= 0.337 Chirality : 0.045 0.282 1793 Planarity : 0.005 0.043 2119 Dihedral : 8.603 74.509 1849 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 1.79 % Allowed : 8.40 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1522 helix: 1.40 (0.29), residues: 302 sheet: -1.30 (0.24), residues: 429 loop : -0.95 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 204 HIS 0.012 0.001 HIS C 153 PHE 0.019 0.002 PHE T 236 TYR 0.024 0.002 TYR B 67 ARG 0.011 0.001 ARG M 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 2) link_NAG-ASN : angle 2.24504 ( 6) link_BETA1-4 : bond 0.00431 ( 4) link_BETA1-4 : angle 2.79890 ( 12) link_ALPHA1-2 : bond 0.00934 ( 2) link_ALPHA1-2 : angle 1.72999 ( 6) link_ALPHA1-3 : bond 0.00402 ( 2) link_ALPHA1-3 : angle 2.17095 ( 6) hydrogen bonds : bond 0.04090 ( 462) hydrogen bonds : angle 5.56220 ( 1230) SS BOND : bond 0.00536 ( 9) SS BOND : angle 1.51583 ( 18) covalent geometry : bond 0.00356 (11838) covalent geometry : angle 0.66713 (16173) *********************** 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 156 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.7264 (mt) cc_final: 0.6888 (mt) REVERT: T 87 SER cc_start: 0.8619 (p) cc_final: 0.8361 (t) REVERT: C 321 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.7032 (t80) REVERT: C 349 ARG cc_start: 0.8747 (tmm-80) cc_final: 0.8326 (tmm-80) outliers start: 19 outliers final: 10 residues processed: 146 average time/residue: 0.2250 time to fit residues: 47.7424 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 : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 213 GLU 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 3 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.113989 restraints weight = 19611.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106544 restraints weight = 26856.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103508 restraints weight = 21443.100| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11857 Z= 0.238 Angle : 0.709 9.862 16221 Z= 0.352 Chirality : 0.046 0.328 1793 Planarity : 0.005 0.047 2119 Dihedral : 7.659 63.565 1848 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 1.98 % Allowed : 11.79 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1522 helix: 1.33 (0.30), residues: 306 sheet: -1.25 (0.25), residues: 430 loop : -0.99 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 204 HIS 0.006 0.001 HIS B 51 PHE 0.026 0.002 PHE B 30 TYR 0.030 0.002 TYR B 67 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 2) link_NAG-ASN : angle 2.97632 ( 6) link_BETA1-4 : bond 0.00289 ( 4) link_BETA1-4 : angle 2.99559 ( 12) link_ALPHA1-2 : bond 0.00511 ( 2) link_ALPHA1-2 : angle 1.63914 ( 6) link_ALPHA1-3 : bond 0.00301 ( 2) link_ALPHA1-3 : angle 2.03725 ( 6) hydrogen bonds : bond 0.04062 ( 462) hydrogen bonds : angle 5.46957 ( 1230) SS BOND : bond 0.00627 ( 9) SS BOND : angle 1.81847 ( 18) covalent geometry : bond 0.00542 (11838) covalent geometry : angle 0.69839 (16173) *********************** 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 149 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ASN cc_start: 0.7430 (t0) cc_final: 0.7210 (t0) REVERT: B 98 ASP cc_start: 0.8163 (m-30) cc_final: 0.7952 (m-30) REVERT: T 40 LEU cc_start: 0.7444 (mt) cc_final: 0.6961 (mt) REVERT: T 87 SER cc_start: 0.8719 (p) cc_final: 0.8410 (t) REVERT: C 254 TYR cc_start: 0.5604 (t80) cc_final: 0.4798 (t80) outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 0.2153 time to fit residues: 43.8239 Evaluate side-chains 133 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 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 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 52 SER Chi-restraints excluded: chain C residue 61 SER 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 116 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 345 HIS C 173 GLN C 303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.149697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.117261 restraints weight = 19476.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.109674 restraints weight = 24245.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107090 restraints weight = 20277.498| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11857 Z= 0.160 Angle : 0.663 14.154 16221 Z= 0.321 Chirality : 0.044 0.293 1793 Planarity : 0.005 0.046 2119 Dihedral : 6.595 58.243 1848 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 2.17 % Allowed : 13.11 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1522 helix: 1.44 (0.29), residues: 312 sheet: -1.08 (0.25), residues: 439 loop : -0.99 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 204 HIS 0.004 0.001 HIS C 153 PHE 0.024 0.002 PHE C 115 TYR 0.025 0.002 TYR B 67 ARG 0.011 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 2) link_NAG-ASN : angle 2.43419 ( 6) link_BETA1-4 : bond 0.00419 ( 4) link_BETA1-4 : angle 2.72411 ( 12) link_ALPHA1-2 : bond 0.00666 ( 2) link_ALPHA1-2 : angle 1.59318 ( 6) link_ALPHA1-3 : bond 0.00453 ( 2) link_ALPHA1-3 : angle 1.86199 ( 6) hydrogen bonds : bond 0.03573 ( 462) hydrogen bonds : angle 5.23920 ( 1230) SS BOND : bond 0.00716 ( 9) SS BOND : angle 1.94122 ( 18) covalent geometry : bond 0.00366 (11838) covalent geometry : angle 0.65363 (16173) *********************** 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 156 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 ASN cc_start: 0.7204 (t0) cc_final: 0.6992 (m-40) REVERT: T 40 LEU cc_start: 0.7552 (mt) cc_final: 0.7107 (mt) REVERT: T 87 SER cc_start: 0.8564 (p) cc_final: 0.8238 (t) REVERT: T 347 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8861 (tp40) REVERT: E 24 MET cc_start: 0.4555 (tpt) cc_final: 0.4255 (tpp) REVERT: C 254 TYR cc_start: 0.5263 (t80) cc_final: 0.4574 (t80) REVERT: C 340 MET cc_start: 0.7835 (ptm) cc_final: 0.7553 (ptm) REVERT: C 349 ARG cc_start: 0.8740 (tmm-80) cc_final: 0.8291 (tmm-80) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 0.2173 time to fit residues: 46.9417 Evaluate side-chains 129 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 132 ILE 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 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 95 LEU 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 24 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** M 72 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.149340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114987 restraints weight = 19447.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109895 restraints weight = 25587.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105687 restraints weight = 18798.792| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11857 Z= 0.162 Angle : 0.661 15.055 16221 Z= 0.325 Chirality : 0.043 0.297 1793 Planarity : 0.005 0.048 2119 Dihedral : 6.423 58.272 1848 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 2.17 % Allowed : 14.81 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1522 helix: 1.45 (0.29), residues: 312 sheet: -1.03 (0.25), residues: 439 loop : -1.00 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 204 HIS 0.007 0.001 HIS M 192 PHE 0.022 0.002 PHE C 115 TYR 0.026 0.001 TYR B 67 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 2) link_NAG-ASN : angle 2.48879 ( 6) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 2.52164 ( 12) link_ALPHA1-2 : bond 0.00579 ( 2) link_ALPHA1-2 : angle 1.64029 ( 6) link_ALPHA1-3 : bond 0.00429 ( 2) link_ALPHA1-3 : angle 1.90610 ( 6) hydrogen bonds : bond 0.03484 ( 462) hydrogen bonds : angle 5.14167 ( 1230) SS BOND : bond 0.00546 ( 9) SS BOND : angle 2.93702 ( 18) covalent geometry : bond 0.00371 (11838) covalent geometry : angle 0.64730 (16173) *********************** 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 150 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.7509 (mt) cc_final: 0.7058 (mt) REVERT: T 87 SER cc_start: 0.8676 (p) cc_final: 0.8381 (t) REVERT: T 347 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8696 (tp40) REVERT: C 254 TYR cc_start: 0.5026 (t80) cc_final: 0.4304 (t80) REVERT: C 340 MET cc_start: 0.7738 (ptm) cc_final: 0.7461 (ptm) REVERT: C 349 ARG cc_start: 0.8737 (tmm-80) cc_final: 0.8306 (tmm-80) outliers start: 23 outliers final: 17 residues processed: 141 average time/residue: 0.2440 time to fit residues: 50.6946 Evaluate side-chains 132 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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 E residue 190 LYS Chi-restraints excluded: chain M residue 134 THR 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 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 95 LEU 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 105 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.150019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.115968 restraints weight = 19515.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110431 restraints weight = 25068.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107170 restraints weight = 18809.637| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11857 Z= 0.140 Angle : 0.633 11.879 16221 Z= 0.309 Chirality : 0.043 0.286 1793 Planarity : 0.005 0.050 2119 Dihedral : 6.133 58.472 1848 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 2.17 % Allowed : 14.81 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1522 helix: 1.58 (0.29), residues: 312 sheet: -0.89 (0.26), residues: 410 loop : -1.02 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 204 HIS 0.004 0.001 HIS B 84 PHE 0.026 0.002 PHE C 115 TYR 0.025 0.001 TYR B 67 ARG 0.008 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 2) link_NAG-ASN : angle 2.32975 ( 6) link_BETA1-4 : bond 0.00298 ( 4) link_BETA1-4 : angle 2.44120 ( 12) link_ALPHA1-2 : bond 0.00701 ( 2) link_ALPHA1-2 : angle 1.62589 ( 6) link_ALPHA1-3 : bond 0.00684 ( 2) link_ALPHA1-3 : angle 1.71632 ( 6) hydrogen bonds : bond 0.03299 ( 462) hydrogen bonds : angle 4.98006 ( 1230) SS BOND : bond 0.00454 ( 9) SS BOND : angle 1.93626 ( 18) covalent geometry : bond 0.00322 (11838) covalent geometry : angle 0.62359 (16173) *********************** 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: 23 poor density : 125 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.7523 (mt) cc_final: 0.7082 (mt) REVERT: T 87 SER cc_start: 0.8477 (p) cc_final: 0.8170 (t) REVERT: T 165 MET cc_start: 0.6681 (tpp) cc_final: 0.6378 (tpp) REVERT: E 160 PHE cc_start: 0.7407 (m-80) cc_final: 0.6842 (m-80) REVERT: C 254 TYR cc_start: 0.5259 (t80) cc_final: 0.4591 (t80) REVERT: C 349 ARG cc_start: 0.8717 (tmm-80) cc_final: 0.8279 (tmm-80) outliers start: 23 outliers final: 20 residues processed: 138 average time/residue: 0.2387 time to fit residues: 48.3607 Evaluate side-chains 131 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 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 E residue 190 LYS 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 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 126 LYS Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 134 optimal weight: 0.0040 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.148553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114031 restraints weight = 19729.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109656 restraints weight = 25689.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 85)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104347 restraints weight = 16451.294| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11857 Z= 0.177 Angle : 0.652 10.578 16221 Z= 0.320 Chirality : 0.043 0.307 1793 Planarity : 0.005 0.049 2119 Dihedral : 5.925 58.331 1848 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 2.55 % Allowed : 15.57 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1522 helix: 1.56 (0.29), residues: 312 sheet: -0.91 (0.26), residues: 411 loop : -1.02 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 244 HIS 0.005 0.001 HIS C 128 PHE 0.023 0.002 PHE C 115 TYR 0.025 0.002 TYR B 67 ARG 0.003 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 2) link_NAG-ASN : angle 2.66105 ( 6) link_BETA1-4 : bond 0.00231 ( 4) link_BETA1-4 : angle 2.54385 ( 12) link_ALPHA1-2 : bond 0.00480 ( 2) link_ALPHA1-2 : angle 1.67335 ( 6) link_ALPHA1-3 : bond 0.00414 ( 2) link_ALPHA1-3 : angle 1.65714 ( 6) hydrogen bonds : bond 0.03434 ( 462) hydrogen bonds : angle 5.00712 ( 1230) SS BOND : bond 0.00532 ( 9) SS BOND : angle 1.68792 ( 18) covalent geometry : bond 0.00407 (11838) covalent geometry : angle 0.64305 (16173) *********************** 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 141 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 40 LEU cc_start: 0.7531 (mt) cc_final: 0.7140 (mt) REVERT: T 87 SER cc_start: 0.8648 (p) cc_final: 0.8361 (t) REVERT: T 165 MET cc_start: 0.6898 (tpp) cc_final: 0.6645 (tpp) REVERT: T 326 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: E 160 PHE cc_start: 0.7356 (m-80) cc_final: 0.6783 (m-80) REVERT: C 254 TYR cc_start: 0.5016 (t80) cc_final: 0.4328 (t80) REVERT: C 349 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8259 (tmm-80) outliers start: 27 outliers final: 23 residues processed: 129 average time/residue: 0.2232 time to fit residues: 43.5388 Evaluate side-chains 137 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 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 T residue 340 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 190 LYS 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 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 92 TYR Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 136 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.149769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116620 restraints weight = 19450.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104770 restraints weight = 24029.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104942 restraints weight = 23678.486| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3108 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= 0.138 Angle : 0.637 11.121 16221 Z= 0.311 Chirality : 0.042 0.286 1793 Planarity : 0.005 0.051 2119 Dihedral : 5.732 58.773 1848 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 2.17 % Allowed : 15.28 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1522 helix: 1.66 (0.29), residues: 312 sheet: -0.88 (0.26), residues: 410 loop : -0.99 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 204 HIS 0.004 0.001 HIS M 191 PHE 0.021 0.001 PHE C 115 TYR 0.024 0.001 TYR B 67 ARG 0.005 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 2) link_NAG-ASN : angle 2.37794 ( 6) link_BETA1-4 : bond 0.00296 ( 4) link_BETA1-4 : angle 2.45910 ( 12) link_ALPHA1-2 : bond 0.00444 ( 2) link_ALPHA1-2 : angle 1.60030 ( 6) link_ALPHA1-3 : bond 0.00427 ( 2) link_ALPHA1-3 : angle 1.77274 ( 6) hydrogen bonds : bond 0.03291 ( 462) hydrogen bonds : angle 4.90619 ( 1230) SS BOND : bond 0.00464 ( 9) SS BOND : angle 1.54758 ( 18) covalent geometry : bond 0.00320 (11838) covalent geometry : angle 0.62906 (16173) *********************** 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 142 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7645 (t0) cc_final: 0.7401 (t0) REVERT: T 40 LEU cc_start: 0.7561 (mt) cc_final: 0.7139 (mt) REVERT: T 87 SER cc_start: 0.8586 (p) cc_final: 0.8286 (t) REVERT: T 165 MET cc_start: 0.6909 (tpp) cc_final: 0.6657 (tpp) REVERT: E 160 PHE cc_start: 0.7511 (m-80) cc_final: 0.6989 (m-80) REVERT: C 254 TYR cc_start: 0.5417 (t80) cc_final: 0.4776 (t80) REVERT: C 349 ARG cc_start: 0.8695 (tmm-80) cc_final: 0.8244 (tmm-80) outliers start: 23 outliers final: 21 residues processed: 133 average time/residue: 0.2711 time to fit residues: 52.8026 Evaluate side-chains 134 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.672 ------------------------------------------------------------------------------- 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 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 340 VAL Chi-restraints excluded: chain E residue 190 LYS 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 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 126 LYS 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 14 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.149213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.115962 restraints weight = 19807.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103822 restraints weight = 25662.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104451 restraints weight = 25548.254| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11857 Z= 0.160 Angle : 0.649 9.591 16221 Z= 0.320 Chirality : 0.043 0.295 1793 Planarity : 0.005 0.050 2119 Dihedral : 5.648 58.426 1848 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 2.17 % Allowed : 15.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1522 helix: 1.66 (0.29), residues: 312 sheet: -0.90 (0.26), residues: 410 loop : -0.98 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 302 HIS 0.004 0.001 HIS B 51 PHE 0.026 0.002 PHE C 115 TYR 0.028 0.002 TYR B 67 ARG 0.006 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 2) link_NAG-ASN : angle 2.52422 ( 6) link_BETA1-4 : bond 0.00273 ( 4) link_BETA1-4 : angle 2.48056 ( 12) link_ALPHA1-2 : bond 0.00506 ( 2) link_ALPHA1-2 : angle 1.69747 ( 6) link_ALPHA1-3 : bond 0.00395 ( 2) link_ALPHA1-3 : angle 1.84631 ( 6) hydrogen bonds : bond 0.03360 ( 462) hydrogen bonds : angle 4.91959 ( 1230) SS BOND : bond 0.00478 ( 9) SS BOND : angle 1.53854 ( 18) covalent geometry : bond 0.00372 (11838) covalent geometry : angle 0.64094 (16173) *********************** 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 142 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7583 (t0) cc_final: 0.7322 (t0) REVERT: T 87 SER cc_start: 0.8613 (p) cc_final: 0.8306 (t) REVERT: E 24 MET cc_start: 0.4426 (tpt) cc_final: 0.4133 (tpp) REVERT: E 160 PHE cc_start: 0.7458 (m-80) cc_final: 0.6917 (m-80) REVERT: C 254 TYR cc_start: 0.5051 (t80) cc_final: 0.4355 (t80) REVERT: C 349 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8243 (tmm-80) outliers start: 23 outliers final: 23 residues processed: 132 average time/residue: 0.2337 time to fit residues: 45.4468 Evaluate side-chains 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 340 VAL Chi-restraints excluded: chain E residue 190 LYS 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 187 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 126 LYS Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 150 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 0.0770 chunk 148 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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** M 260 HIS C 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.149622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116701 restraints weight = 19673.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.107651 restraints weight = 25188.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105143 restraints weight = 20881.373| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11857 Z= 0.151 Angle : 0.655 11.409 16221 Z= 0.321 Chirality : 0.043 0.287 1793 Planarity : 0.005 0.051 2119 Dihedral : 5.505 58.541 1848 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 2.45 % Allowed : 16.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1522 helix: 1.72 (0.29), residues: 312 sheet: -0.87 (0.26), residues: 410 loop : -0.97 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP M 51 HIS 0.004 0.001 HIS B 51 PHE 0.029 0.002 PHE C 115 TYR 0.027 0.002 TYR B 67 ARG 0.006 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 2) link_NAG-ASN : angle 2.42864 ( 6) link_BETA1-4 : bond 0.00263 ( 4) link_BETA1-4 : angle 2.43478 ( 12) link_ALPHA1-2 : bond 0.00525 ( 2) link_ALPHA1-2 : angle 1.60706 ( 6) link_ALPHA1-3 : bond 0.00578 ( 2) link_ALPHA1-3 : angle 1.58950 ( 6) hydrogen bonds : bond 0.03289 ( 462) hydrogen bonds : angle 4.88163 ( 1230) SS BOND : bond 0.00456 ( 9) SS BOND : angle 1.49660 ( 18) covalent geometry : bond 0.00352 (11838) covalent geometry : angle 0.64777 (16173) ********************** 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 147 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.7612 (t0) cc_final: 0.7388 (t0) REVERT: T 87 SER cc_start: 0.8568 (p) cc_final: 0.8249 (t) REVERT: E 24 MET cc_start: 0.4561 (tpt) cc_final: 0.4318 (tpp) REVERT: E 160 PHE cc_start: 0.7513 (m-80) cc_final: 0.6996 (m-80) REVERT: E 314 MET cc_start: 0.6342 (mtp) cc_final: 0.6100 (mtt) REVERT: C 240 MET cc_start: 0.5114 (ppp) cc_final: 0.4795 (ppp) REVERT: C 254 TYR cc_start: 0.5184 (t80) cc_final: 0.4451 (t80) REVERT: C 349 ARG cc_start: 0.8641 (tmm-80) cc_final: 0.8269 (tmm-80) outliers start: 26 outliers final: 25 residues processed: 136 average time/residue: 0.2815 time to fit residues: 58.0280 Evaluate side-chains 141 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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 340 VAL Chi-restraints excluded: chain E residue 190 LYS 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 187 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 92 TYR Chi-restraints excluded: chain C residue 126 LYS 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 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.0770 chunk 26 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 E 35 HIS ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.150435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117461 restraints weight = 19519.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108948 restraints weight = 24968.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109039 restraints weight = 25845.393| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11857 Z= 0.132 Angle : 0.653 9.946 16221 Z= 0.316 Chirality : 0.045 0.553 1793 Planarity : 0.005 0.051 2119 Dihedral : 5.341 58.668 1848 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 2.26 % Allowed : 16.42 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1522 helix: 1.76 (0.29), residues: 312 sheet: -0.88 (0.26), residues: 430 loop : -0.87 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP M 51 HIS 0.004 0.001 HIS M 191 PHE 0.024 0.001 PHE C 115 TYR 0.026 0.001 TYR B 67 ARG 0.005 0.000 ARG C 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 2) link_NAG-ASN : angle 2.22683 ( 6) link_BETA1-4 : bond 0.00303 ( 4) link_BETA1-4 : angle 2.33921 ( 12) link_ALPHA1-2 : bond 0.00567 ( 2) link_ALPHA1-2 : angle 1.58376 ( 6) link_ALPHA1-3 : bond 0.00528 ( 2) link_ALPHA1-3 : angle 1.59551 ( 6) hydrogen bonds : bond 0.03210 ( 462) hydrogen bonds : angle 4.84480 ( 1230) SS BOND : bond 0.00567 ( 9) SS BOND : angle 2.19960 ( 18) covalent geometry : bond 0.00312 (11838) covalent geometry : angle 0.64370 (16173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.77 seconds wall clock time: 86 minutes 45.30 seconds (5205.30 seconds total)