Starting phenix.real_space_refine on Sun Aug 24 22:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4b_41877/08_2025/8u4b_41877_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4b_41877/08_2025/8u4b_41877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u4b_41877/08_2025/8u4b_41877_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4b_41877/08_2025/8u4b_41877_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u4b_41877/08_2025/8u4b_41877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4b_41877/08_2025/8u4b_41877.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12534 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 8388 2.51 5 N 2284 2.21 5 O 2444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13212 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6606 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 774} Chain breaks: 5 Chain: "B" Number of atoms: 6606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6606 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 774} Chain breaks: 5 Time building chain proxies: 3.18, per 1000 atoms: 0.24 Number of scatterers: 13212 At special positions: 0 Unit cell: (89.64, 147.96, 141.48, 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 96 16.00 O 2444 8.00 N 2284 7.00 C 8388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 872 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 807 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 576.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3084 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 28 sheets defined 14.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.681A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.894A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 47' Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.379A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.954A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.620A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.777A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 446 removed outlier: 4.036A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.053A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'A' and resid 875 through 882 Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.683A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.895A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 47' Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.385A pdb=" N ASP B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.955A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 removed outlier: 4.136A pdb=" N ASN B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.777A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 435 through 446 removed outlier: 4.053A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 639 through 644 removed outlier: 4.111A pdb=" N GLU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'B' and resid 874 through 882 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.494A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 37 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR A 91 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ARG A 118 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 146 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 321 removed outlier: 10.304A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 10.304A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.588A pdb=" N TYR A 477 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 485 " --> pdb=" O MET A 553 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 534 Processing sheet with id=AB2, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.876A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 611 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 771 through 772 removed outlier: 3.611A pdb=" N GLU A 772 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 630 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 790 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 831 through 834 removed outlier: 3.639A pdb=" N CYS A 884 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 868 through 874 removed outlier: 3.838A pdb=" N LEU A 856 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 896 " --> pdb=" O THR A 913 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 913 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.497A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 146 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AB9, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC1, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC2, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 321 removed outlier: 10.307A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321 removed outlier: 10.307A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 475 through 480 removed outlier: 3.596A pdb=" N TYR B 477 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 485 " --> pdb=" O MET B 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 530 through 534 Processing sheet with id=AC7, first strand: chain 'B' and resid 599 through 605 removed outlier: 5.876A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 611 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 771 through 772 removed outlier: 3.545A pdb=" N GLU B 772 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 630 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 790 " --> pdb=" O GLN B 635 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 831 through 834 removed outlier: 3.654A pdb=" N CYS B 884 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 868 through 873 removed outlier: 3.838A pdb=" N LEU B 856 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 896 " --> pdb=" O THR B 913 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 913 " --> pdb=" O VAL B 896 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 840 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: 2.76 Time building geometry restraints manager: 1.47 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: 4336 1.34 - 1.46: 2980 1.46 - 1.58: 6100 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 13534 Sorted by residual: bond pdb=" CA GLN A 465 " pdb=" C GLN A 465 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.56e-02 4.11e+03 3.42e+00 bond pdb=" C PRO A 307 " pdb=" N CYS A 308 " ideal model delta sigma weight residual 1.329 1.314 0.015 1.35e-02 5.49e+03 1.28e+00 bond pdb=" C PRO B 307 " pdb=" N CYS B 308 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.59e-02 3.96e+03 1.20e+00 bond pdb=" CB MET B 294 " pdb=" CG MET B 294 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.92e-01 bond pdb=" CB GLN B 272 " pdb=" CG GLN B 272 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.81e-01 ... (remaining 13529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 18127 2.28 - 4.57: 191 4.57 - 6.85: 19 6.85 - 9.13: 5 9.13 - 11.42: 2 Bond angle restraints: 18344 Sorted by residual: angle pdb=" CB MET B 294 " pdb=" CG MET B 294 " pdb=" SD MET B 294 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " ideal model delta sigma weight residual 112.70 122.55 -9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CA MET B 294 " pdb=" CB MET B 294 " pdb=" CG MET B 294 " ideal model delta sigma weight residual 114.10 120.16 -6.06 2.00e+00 2.50e-01 9.18e+00 angle pdb=" CA MET A 294 " pdb=" CB MET A 294 " pdb=" CG MET A 294 " ideal model delta sigma weight residual 114.10 119.54 -5.44 2.00e+00 2.50e-01 7.39e+00 angle pdb=" CA GLU A 30 " pdb=" CB GLU A 30 " pdb=" CG GLU A 30 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.27e+00 ... (remaining 18339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 7028 17.51 - 35.01: 919 35.01 - 52.52: 218 52.52 - 70.02: 36 70.02 - 87.53: 13 Dihedral angle restraints: 8214 sinusoidal: 3438 harmonic: 4776 Sorted by residual: dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual -86.00 -156.17 70.17 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS B 259 " pdb=" SG CYS B 259 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual -86.00 -155.19 69.19 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS B 304 " pdb=" SG CYS B 304 " pdb=" SG CYS B 308 " pdb=" CB CYS B 308 " ideal model delta sinusoidal sigma weight residual -86.00 -28.86 -57.14 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 8211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1133 0.027 - 0.054: 487 0.054 - 0.080: 180 0.080 - 0.107: 125 0.107 - 0.134: 69 Chirality restraints: 1994 Sorted by residual: chirality pdb=" CA THR A 802 " pdb=" N THR A 802 " pdb=" C THR A 802 " pdb=" CB THR A 802 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 285 " pdb=" N ILE A 285 " pdb=" C ILE A 285 " pdb=" CB ILE A 285 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA THR B 802 " pdb=" N THR B 802 " pdb=" C THR B 802 " pdb=" CB THR B 802 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1991 not shown) Planarity restraints: 2368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 285 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 286 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 285 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 286 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 306 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO B 307 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.022 5.00e-02 4.00e+02 ... (remaining 2365 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 396 2.70 - 3.25: 13126 3.25 - 3.80: 21020 3.80 - 4.35: 26581 4.35 - 4.90: 43111 Nonbonded interactions: 104234 Sorted by model distance: nonbonded pdb=" OG SER B 399 " pdb=" O GLN B 423 " model vdw 2.146 3.040 nonbonded pdb=" OH TYR A 127 " pdb=" O ILE A 158 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR B 127 " pdb=" O ILE B 158 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 374 " pdb=" OH TYR B 374 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN A 295 " pdb=" OG SER A 297 " model vdw 2.234 3.040 ... (remaining 104229 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.003 0.040 13568 Z= 0.137 Angle : 0.597 11.416 18412 Z= 0.306 Chirality : 0.044 0.134 1994 Planarity : 0.003 0.045 2368 Dihedral : 16.017 87.531 5028 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 0.07 % Allowed : 24.43 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.22), residues: 1610 helix: 0.35 (0.45), residues: 158 sheet: -0.23 (0.28), residues: 346 loop : -0.94 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 577 TYR 0.011 0.001 TYR B 864 PHE 0.013 0.001 PHE A 705 TRP 0.026 0.001 TRP A 414 HIS 0.007 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00297 (13534) covalent geometry : angle 0.59408 (18344) SS BOND : bond 0.00212 ( 34) SS BOND : angle 1.16631 ( 68) hydrogen bonds : bond 0.24175 ( 311) hydrogen bonds : angle 9.04833 ( 840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7348 (mmt) cc_final: 0.6964 (mmt) REVERT: A 703 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8845 (tppp) REVERT: B 38 MET cc_start: 0.7412 (mmt) cc_final: 0.7036 (mmt) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1018 time to fit residues: 5.9056 Evaluate side-chains 31 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 703 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 837 ASN B 610 GLN B 837 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.073427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055102 restraints weight = 50942.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.056819 restraints weight = 31911.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.057974 restraints weight = 23610.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058721 restraints weight = 19343.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059245 restraints weight = 16962.625| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13568 Z= 0.126 Angle : 0.580 7.665 18412 Z= 0.298 Chirality : 0.045 0.155 1994 Planarity : 0.004 0.044 2368 Dihedral : 4.388 46.478 1794 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.27 % Favored : 93.60 % Rotamer: Outliers : 1.75 % Allowed : 21.80 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.22), residues: 1610 helix: 1.05 (0.48), residues: 150 sheet: -0.25 (0.26), residues: 390 loop : -0.91 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 577 TYR 0.011 0.001 TYR A 507 PHE 0.013 0.001 PHE A 631 TRP 0.018 0.001 TRP A 414 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00281 (13534) covalent geometry : angle 0.57827 (18344) SS BOND : bond 0.00209 ( 34) SS BOND : angle 0.92686 ( 68) hydrogen bonds : bond 0.04859 ( 311) hydrogen bonds : angle 6.84324 ( 840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7695 (mmt) cc_final: 0.7007 (mmt) REVERT: A 373 SER cc_start: 0.9442 (t) cc_final: 0.9200 (p) REVERT: A 553 MET cc_start: 0.8162 (mmm) cc_final: 0.7636 (mtt) REVERT: B 38 MET cc_start: 0.7752 (mmt) cc_final: 0.7053 (mmt) REVERT: B 373 SER cc_start: 0.9419 (t) cc_final: 0.9190 (p) REVERT: B 553 MET cc_start: 0.8101 (mmm) cc_final: 0.7562 (mtt) outliers start: 26 outliers final: 3 residues processed: 60 average time/residue: 0.0858 time to fit residues: 8.6632 Evaluate side-chains 34 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 798 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 440 HIS B 100 HIS B 263 HIS B 431 ASN B 440 HIS B 796 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.070412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.052637 restraints weight = 51895.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053882 restraints weight = 33121.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054348 restraints weight = 25493.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054516 restraints weight = 23019.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054769 restraints weight = 21332.254| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13568 Z= 0.339 Angle : 0.716 8.346 18412 Z= 0.366 Chirality : 0.048 0.193 1994 Planarity : 0.004 0.042 2368 Dihedral : 4.862 27.285 1790 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.07 % Favored : 91.80 % Rotamer: Outliers : 3.57 % Allowed : 20.39 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.22), residues: 1610 helix: 0.30 (0.43), residues: 170 sheet: -0.39 (0.26), residues: 376 loop : -1.11 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 577 TYR 0.014 0.002 TYR A 857 PHE 0.024 0.002 PHE B 705 TRP 0.017 0.002 TRP A 414 HIS 0.005 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00767 (13534) covalent geometry : angle 0.71133 (18344) SS BOND : bond 0.00660 ( 34) SS BOND : angle 1.58115 ( 68) hydrogen bonds : bond 0.05270 ( 311) hydrogen bonds : angle 6.54221 ( 840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 39 time to evaluate : 0.547 Fit side-chains REVERT: A 38 MET cc_start: 0.7951 (mmt) cc_final: 0.7539 (mmt) REVERT: A 845 GLN cc_start: 0.8356 (tp40) cc_final: 0.7988 (tp40) REVERT: A 882 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8372 (tpm170) REVERT: B 38 MET cc_start: 0.8000 (mmt) cc_final: 0.7532 (mmt) REVERT: B 882 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8166 (tpt90) outliers start: 53 outliers final: 25 residues processed: 88 average time/residue: 0.1105 time to fit residues: 15.1400 Evaluate side-chains 59 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 32 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 247 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 914 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 147 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 431 ASN A 610 GLN B 796 GLN B 877 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.072909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.054160 restraints weight = 50586.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055819 restraints weight = 31352.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.056938 restraints weight = 23161.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.057632 restraints weight = 19065.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.058153 restraints weight = 16875.045| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13568 Z= 0.119 Angle : 0.582 11.893 18412 Z= 0.293 Chirality : 0.045 0.165 1994 Planarity : 0.003 0.045 2368 Dihedral : 4.488 23.622 1790 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 2.09 % Allowed : 22.54 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.22), residues: 1610 helix: 0.60 (0.44), residues: 158 sheet: -0.28 (0.27), residues: 376 loop : -1.01 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 577 TYR 0.014 0.001 TYR A 507 PHE 0.013 0.001 PHE B 705 TRP 0.016 0.001 TRP A 414 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00265 (13534) covalent geometry : angle 0.57852 (18344) SS BOND : bond 0.00379 ( 34) SS BOND : angle 1.24923 ( 68) hydrogen bonds : bond 0.04033 ( 311) hydrogen bonds : angle 6.19070 ( 840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 32 time to evaluate : 0.560 Fit side-chains REVERT: A 38 MET cc_start: 0.7983 (mmt) cc_final: 0.7452 (mmt) REVERT: A 166 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5392 (tptp) REVERT: A 553 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7929 (mmm) REVERT: B 38 MET cc_start: 0.7995 (mmt) cc_final: 0.7438 (mmt) REVERT: B 846 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8556 (pm20) outliers start: 31 outliers final: 10 residues processed: 61 average time/residue: 0.0827 time to fit residues: 8.6743 Evaluate side-chains 44 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 846 GLU Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 43 optimal weight: 0.0370 chunk 118 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 147 optimal weight: 0.0470 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 877 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.071182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052437 restraints weight = 51258.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054857 restraints weight = 30986.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055019 restraints weight = 21410.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055400 restraints weight = 19074.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055530 restraints weight = 17402.505| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13568 Z= 0.254 Angle : 0.643 8.690 18412 Z= 0.325 Chirality : 0.046 0.184 1994 Planarity : 0.004 0.044 2368 Dihedral : 4.753 24.831 1790 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 2.83 % Allowed : 21.87 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.22), residues: 1610 helix: 0.53 (0.45), residues: 158 sheet: -0.37 (0.27), residues: 376 loop : -1.06 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 577 TYR 0.012 0.001 TYR B 857 PHE 0.019 0.002 PHE B 705 TRP 0.014 0.001 TRP A 414 HIS 0.003 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00581 (13534) covalent geometry : angle 0.63687 (18344) SS BOND : bond 0.00461 ( 34) SS BOND : angle 1.63794 ( 68) hydrogen bonds : bond 0.04404 ( 311) hydrogen bonds : angle 6.19334 ( 840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 31 time to evaluate : 0.455 Fit side-chains REVERT: A 38 MET cc_start: 0.8051 (mmt) cc_final: 0.7645 (mmt) REVERT: A 61 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 166 LYS cc_start: 0.5719 (OUTLIER) cc_final: 0.5515 (tptt) REVERT: A 553 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8343 (mmm) REVERT: A 882 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8455 (tpm170) REVERT: B 38 MET cc_start: 0.8059 (mmt) cc_final: 0.7626 (mmt) REVERT: B 61 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8707 (tt) REVERT: B 553 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8294 (mmm) REVERT: B 882 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8098 (tpt90) outliers start: 42 outliers final: 25 residues processed: 69 average time/residue: 0.1073 time to fit residues: 11.7683 Evaluate side-chains 63 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 31 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 247 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 914 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 25 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 796 GLN B 877 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.072203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053166 restraints weight = 50452.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054855 restraints weight = 30930.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.055980 restraints weight = 22865.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.056725 restraints weight = 18821.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057217 restraints weight = 16541.972| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13568 Z= 0.145 Angle : 0.589 13.194 18412 Z= 0.293 Chirality : 0.045 0.146 1994 Planarity : 0.003 0.046 2368 Dihedral : 4.578 23.035 1790 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 2.62 % Allowed : 21.60 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.22), residues: 1610 helix: 0.59 (0.44), residues: 158 sheet: -0.38 (0.27), residues: 376 loop : -1.00 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.013 0.001 TYR A 507 PHE 0.015 0.001 PHE B 705 TRP 0.015 0.001 TRP A 414 HIS 0.003 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00335 (13534) covalent geometry : angle 0.58562 (18344) SS BOND : bond 0.00292 ( 34) SS BOND : angle 1.22447 ( 68) hydrogen bonds : bond 0.03852 ( 311) hydrogen bonds : angle 5.99630 ( 840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 36 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7963 (mmt) cc_final: 0.7388 (mmt) REVERT: A 166 LYS cc_start: 0.5417 (OUTLIER) cc_final: 0.5197 (tptt) REVERT: A 553 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8074 (mmm) REVERT: A 882 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8389 (tpm170) REVERT: B 38 MET cc_start: 0.8024 (mmt) cc_final: 0.7447 (mmt) REVERT: B 553 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8038 (mmm) REVERT: B 882 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8054 (tpt90) outliers start: 39 outliers final: 24 residues processed: 71 average time/residue: 0.0968 time to fit residues: 11.1507 Evaluate side-chains 62 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 33 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 914 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 21 optimal weight: 0.0020 chunk 16 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 796 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.072245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053798 restraints weight = 50439.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.055916 restraints weight = 29863.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056645 restraints weight = 20693.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056913 restraints weight = 18052.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057156 restraints weight = 16712.878| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13568 Z= 0.141 Angle : 0.580 11.482 18412 Z= 0.289 Chirality : 0.045 0.144 1994 Planarity : 0.003 0.045 2368 Dihedral : 4.472 20.623 1790 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Rotamer: Outliers : 2.76 % Allowed : 21.87 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.22), residues: 1610 helix: 0.67 (0.45), residues: 158 sheet: -0.40 (0.27), residues: 376 loop : -0.98 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 451 TYR 0.012 0.001 TYR A 507 PHE 0.014 0.001 PHE B 705 TRP 0.015 0.001 TRP B 414 HIS 0.004 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00326 (13534) covalent geometry : angle 0.57697 (18344) SS BOND : bond 0.00259 ( 34) SS BOND : angle 1.17555 ( 68) hydrogen bonds : bond 0.03706 ( 311) hydrogen bonds : angle 5.85721 ( 840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 34 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7972 (mmt) cc_final: 0.7381 (mmt) REVERT: A 553 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8084 (mmm) REVERT: B 38 MET cc_start: 0.8053 (mmt) cc_final: 0.7492 (mmt) REVERT: B 553 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8028 (mmm) REVERT: B 882 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7998 (tpt90) outliers start: 41 outliers final: 28 residues processed: 71 average time/residue: 0.0935 time to fit residues: 11.1344 Evaluate side-chains 62 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 31 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 914 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.072333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053642 restraints weight = 49978.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.055289 restraints weight = 31146.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.056385 restraints weight = 23186.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057123 restraints weight = 19113.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057603 restraints weight = 16816.670| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13568 Z= 0.137 Angle : 0.588 10.694 18412 Z= 0.291 Chirality : 0.045 0.142 1994 Planarity : 0.003 0.045 2368 Dihedral : 4.531 30.577 1790 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Rotamer: Outliers : 2.69 % Allowed : 21.87 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.22), residues: 1610 helix: 0.64 (0.44), residues: 158 sheet: -0.36 (0.27), residues: 376 loop : -0.95 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.012 0.001 TYR A 507 PHE 0.014 0.001 PHE B 705 TRP 0.017 0.001 TRP B 414 HIS 0.004 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00319 (13534) covalent geometry : angle 0.58344 (18344) SS BOND : bond 0.00215 ( 34) SS BOND : angle 1.30807 ( 68) hydrogen bonds : bond 0.03634 ( 311) hydrogen bonds : angle 5.85014 ( 840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 32 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7965 (mmt) cc_final: 0.7395 (mmt) REVERT: A 553 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: B 38 MET cc_start: 0.8003 (mmt) cc_final: 0.7425 (mmt) REVERT: B 553 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8039 (mmm) outliers start: 40 outliers final: 25 residues processed: 68 average time/residue: 0.0930 time to fit residues: 10.4609 Evaluate side-chains 59 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 32 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 914 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 47 optimal weight: 4.9990 chunk 133 optimal weight: 0.0270 chunk 122 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 49 optimal weight: 0.0470 chunk 85 optimal weight: 0.0030 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN B 455 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.073431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054687 restraints weight = 50476.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056451 restraints weight = 30423.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.057631 restraints weight = 22185.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058412 restraints weight = 18063.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058922 restraints weight = 15765.909| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 13568 Z= 0.097 Angle : 0.605 11.136 18412 Z= 0.295 Chirality : 0.044 0.143 1994 Planarity : 0.003 0.045 2368 Dihedral : 4.399 33.920 1790 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.90 % Favored : 93.98 % Rotamer: Outliers : 1.28 % Allowed : 23.15 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.22), residues: 1610 helix: 0.65 (0.44), residues: 158 sheet: -0.25 (0.27), residues: 366 loop : -0.91 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 806 TYR 0.016 0.001 TYR A 507 PHE 0.010 0.001 PHE B 701 TRP 0.015 0.001 TRP B 414 HIS 0.004 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00234 (13534) covalent geometry : angle 0.60003 (18344) SS BOND : bond 0.00219 ( 34) SS BOND : angle 1.43855 ( 68) hydrogen bonds : bond 0.03304 ( 311) hydrogen bonds : angle 5.65862 ( 840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7898 (mmt) cc_final: 0.7268 (mmt) REVERT: B 38 MET cc_start: 0.7935 (mmt) cc_final: 0.7299 (mmt) REVERT: B 553 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7890 (mmm) outliers start: 19 outliers final: 14 residues processed: 49 average time/residue: 0.0759 time to fit residues: 6.6780 Evaluate side-chains 44 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 146 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.071703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053306 restraints weight = 51037.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055784 restraints weight = 30344.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055953 restraints weight = 20709.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056325 restraints weight = 18590.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056437 restraints weight = 17071.356| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 13568 Z= 0.204 Angle : 0.643 11.351 18412 Z= 0.317 Chirality : 0.045 0.156 1994 Planarity : 0.003 0.043 2368 Dihedral : 4.605 35.116 1790 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Rotamer: Outliers : 1.35 % Allowed : 22.81 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.22), residues: 1610 helix: 0.75 (0.45), residues: 158 sheet: -0.29 (0.27), residues: 376 loop : -0.91 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 451 TYR 0.010 0.001 TYR B 857 PHE 0.018 0.001 PHE A 705 TRP 0.015 0.001 TRP A 414 HIS 0.003 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00472 (13534) covalent geometry : angle 0.63529 (18344) SS BOND : bond 0.00276 ( 34) SS BOND : angle 1.77526 ( 68) hydrogen bonds : bond 0.03809 ( 311) hydrogen bonds : angle 5.79284 ( 840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7917 (mmt) cc_final: 0.7367 (mmt) REVERT: B 38 MET cc_start: 0.7953 (mmt) cc_final: 0.7343 (mmt) REVERT: B 553 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8085 (mmm) outliers start: 20 outliers final: 17 residues processed: 47 average time/residue: 0.0718 time to fit residues: 6.1640 Evaluate side-chains 47 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Chi-restraints excluded: chain B residue 914 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.070889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.051785 restraints weight = 50879.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053445 restraints weight = 31488.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054528 restraints weight = 23359.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055241 restraints weight = 19331.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055617 restraints weight = 17088.006| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13568 Z= 0.228 Angle : 0.693 15.210 18412 Z= 0.340 Chirality : 0.046 0.188 1994 Planarity : 0.004 0.044 2368 Dihedral : 4.908 36.775 1790 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.52 % Favored : 92.36 % Rotamer: Outliers : 1.75 % Allowed : 22.54 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.22), residues: 1610 helix: 0.76 (0.46), residues: 158 sheet: -0.40 (0.27), residues: 376 loop : -0.97 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.010 0.001 TYR B 857 PHE 0.018 0.002 PHE B 705 TRP 0.020 0.001 TRP A 414 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00525 (13534) covalent geometry : angle 0.68449 (18344) SS BOND : bond 0.00331 ( 34) SS BOND : angle 1.89455 ( 68) hydrogen bonds : bond 0.04083 ( 311) hydrogen bonds : angle 6.00300 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1902.24 seconds wall clock time: 33 minutes 45.40 seconds (2025.40 seconds total)