Starting phenix.real_space_refine on Fri Jun 20 04:35:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4b_41877/06_2025/8u4b_41877_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4b_41877/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4b_41877/06_2025/8u4b_41877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4b_41877/06_2025/8u4b_41877.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4b_41877/06_2025/8u4b_41877_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4b_41877/06_2025/8u4b_41877_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.24, per 1000 atoms: 0.55 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.72 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: 4.59 Time building geometry restraints manager: 3.77 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: 0.06 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.200 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (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 TRP 0.026 0.001 TRP A 414 HIS 0.007 0.001 HIS B 264 PHE 0.013 0.001 PHE A 705 TYR 0.011 0.001 TYR B 864 ARG 0.006 0.000 ARG B 577 Details of bonding type rmsd hydrogen bonds : bond 0.24175 ( 311) hydrogen bonds : angle 9.04833 ( 840) SS BOND : bond 0.00212 ( 34) SS BOND : angle 1.16631 ( 68) covalent geometry : bond 0.00297 (13534) covalent geometry : angle 0.59408 (18344) *********************** 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 : 1.587 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: 0.2339 time to fit residues: 14.0236 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 : 1.569 ------------------------------------------------------------------------------- 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 136 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 126 optimal weight: 0.0970 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 94 optimal weight: 0.0370 chunk 147 optimal weight: 0.1980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 837 ASN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.073858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055306 restraints weight = 50262.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057092 restraints weight = 30629.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.058291 restraints weight = 22295.404| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13568 Z= 0.106 Angle : 0.576 7.972 18412 Z= 0.294 Chirality : 0.045 0.156 1994 Planarity : 0.003 0.044 2368 Dihedral : 4.319 47.130 1794 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 1.68 % Allowed : 21.80 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1610 helix: 1.26 (0.48), residues: 146 sheet: -0.24 (0.27), residues: 386 loop : -0.92 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 414 HIS 0.005 0.001 HIS B 264 PHE 0.013 0.001 PHE A 631 TYR 0.013 0.001 TYR A 507 ARG 0.005 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 311) hydrogen bonds : angle 6.88995 ( 840) SS BOND : bond 0.00203 ( 34) SS BOND : angle 0.85207 ( 68) covalent geometry : bond 0.00229 (13534) covalent geometry : angle 0.57472 (18344) *********************** 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: 25 poor density : 35 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7665 (mmt) cc_final: 0.6966 (mmt) REVERT: A 373 SER cc_start: 0.9458 (t) cc_final: 0.9210 (p) REVERT: A 553 MET cc_start: 0.8138 (mmm) cc_final: 0.7553 (mtt) REVERT: B 38 MET cc_start: 0.7725 (mmt) cc_final: 0.7017 (mmt) REVERT: B 373 SER cc_start: 0.9436 (t) cc_final: 0.9197 (p) outliers start: 25 outliers final: 3 residues processed: 60 average time/residue: 0.2033 time to fit residues: 20.8470 Evaluate side-chains 36 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 121 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 139 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 66 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 610 GLN B 263 HIS B 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.071918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053044 restraints weight = 51390.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054642 restraints weight = 32415.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055772 restraints weight = 24255.974| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13568 Z= 0.192 Angle : 0.597 7.730 18412 Z= 0.304 Chirality : 0.046 0.180 1994 Planarity : 0.004 0.043 2368 Dihedral : 4.382 22.401 1790 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 2.56 % Allowed : 21.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1610 helix: 0.98 (0.47), residues: 150 sheet: -0.14 (0.27), residues: 376 loop : -0.95 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 414 HIS 0.004 0.001 HIS B 440 PHE 0.015 0.002 PHE B 705 TYR 0.010 0.001 TYR A 857 ARG 0.007 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 311) hydrogen bonds : angle 6.28002 ( 840) SS BOND : bond 0.00301 ( 34) SS BOND : angle 1.19767 ( 68) covalent geometry : bond 0.00438 (13534) covalent geometry : angle 0.59414 (18344) *********************** 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 74 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 36 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7843 (mmt) cc_final: 0.7251 (mmt) REVERT: B 38 MET cc_start: 0.7898 (mmt) cc_final: 0.7300 (mmt) outliers start: 38 outliers final: 13 residues processed: 72 average time/residue: 0.2021 time to fit residues: 24.6185 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 : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE 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 886 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 279 ILE 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 798 CYS Chi-restraints excluded: chain B residue 886 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 440 HIS B 100 HIS B 440 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.071812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053047 restraints weight = 50369.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054650 restraints weight = 31775.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055725 restraints weight = 23812.686| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13568 Z= 0.234 Angle : 0.611 7.260 18412 Z= 0.314 Chirality : 0.046 0.168 1994 Planarity : 0.004 0.045 2368 Dihedral : 4.614 24.188 1790 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 3.03 % Allowed : 21.33 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1610 helix: 0.72 (0.45), residues: 158 sheet: -0.24 (0.27), residues: 376 loop : -1.01 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 414 HIS 0.003 0.001 HIS B 264 PHE 0.020 0.002 PHE B 705 TYR 0.011 0.001 TYR B 857 ARG 0.005 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 311) hydrogen bonds : angle 6.18755 ( 840) SS BOND : bond 0.00397 ( 34) SS BOND : angle 1.33618 ( 68) covalent geometry : bond 0.00533 (13534) covalent geometry : angle 0.60649 (18344) *********************** 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 78 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 33 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7929 (mmt) cc_final: 0.7486 (mmt) REVERT: A 56 MET cc_start: 0.8253 (tpp) cc_final: 0.7811 (ttt) REVERT: A 61 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8820 (tt) REVERT: A 166 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5336 (tptt) REVERT: A 882 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8450 (tpm170) REVERT: B 38 MET cc_start: 0.7950 (mmt) cc_final: 0.7487 (mmt) REVERT: B 56 MET cc_start: 0.8303 (tpp) cc_final: 0.7841 (ttt) REVERT: B 61 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8806 (tt) REVERT: B 166 LYS cc_start: 0.5600 (OUTLIER) cc_final: 0.5367 (tptt) REVERT: B 882 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8478 (tpm170) outliers start: 45 outliers final: 24 residues processed: 76 average time/residue: 0.2440 time to fit residues: 29.1045 Evaluate side-chains 61 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 31 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 121 LYS 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 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 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 61 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LYS 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 798 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.072930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054160 restraints weight = 50039.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055853 restraints weight = 30975.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056981 restraints weight = 22876.889| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1622 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= 0.112 Angle : 0.551 7.565 18412 Z= 0.280 Chirality : 0.044 0.143 1994 Planarity : 0.003 0.045 2368 Dihedral : 4.386 22.628 1790 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 1.88 % Allowed : 22.68 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1610 helix: 0.74 (0.45), residues: 158 sheet: -0.21 (0.27), residues: 376 loop : -0.97 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 414 HIS 0.003 0.001 HIS A 21 PHE 0.013 0.001 PHE B 705 TYR 0.012 0.001 TYR A 507 ARG 0.004 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 311) hydrogen bonds : angle 5.95431 ( 840) SS BOND : bond 0.00256 ( 34) SS BOND : angle 1.10137 ( 68) covalent geometry : bond 0.00256 (13534) covalent geometry : angle 0.54770 (18344) *********************** 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 62 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 34 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7998 (mmt) cc_final: 0.7451 (mmt) REVERT: A 166 LYS cc_start: 0.5527 (OUTLIER) cc_final: 0.5236 (tptt) REVERT: B 38 MET cc_start: 0.8034 (mmt) cc_final: 0.7436 (mmt) REVERT: B 166 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.5402 (tptt) REVERT: B 882 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8468 (tpm170) outliers start: 28 outliers final: 13 residues processed: 62 average time/residue: 0.2459 time to fit residues: 24.6200 Evaluate side-chains 49 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LYS 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 886 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 chunk 97 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.072522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054516 restraints weight = 51226.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056020 restraints weight = 31117.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056527 restraints weight = 23842.109| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1771 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= 0.147 Angle : 0.568 14.415 18412 Z= 0.284 Chirality : 0.045 0.161 1994 Planarity : 0.003 0.045 2368 Dihedral : 4.381 26.685 1790 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.46 % Favored : 93.42 % Rotamer: Outliers : 2.56 % Allowed : 21.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1610 helix: 0.78 (0.45), residues: 158 sheet: -0.23 (0.27), residues: 376 loop : -0.94 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.003 0.001 HIS A 21 PHE 0.014 0.001 PHE B 705 TYR 0.012 0.001 TYR A 857 ARG 0.003 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 311) hydrogen bonds : angle 5.82976 ( 840) SS BOND : bond 0.00268 ( 34) SS BOND : angle 1.07212 ( 68) covalent geometry : bond 0.00339 (13534) covalent geometry : angle 0.56494 (18344) *********************** 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 73 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 35 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7950 (mmt) cc_final: 0.7369 (mmt) REVERT: A 166 LYS cc_start: 0.5447 (OUTLIER) cc_final: 0.5237 (tptt) REVERT: A 882 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8344 (tpm170) REVERT: B 38 MET cc_start: 0.7996 (mmt) cc_final: 0.7397 (mmt) REVERT: B 166 LYS cc_start: 0.5609 (OUTLIER) cc_final: 0.5375 (tptt) REVERT: B 882 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8371 (tpm170) outliers start: 38 outliers final: 20 residues processed: 73 average time/residue: 0.2607 time to fit residues: 29.4899 Evaluate side-chains 55 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 789 THR 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 B residue 121 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 279 ILE 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 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 886 LEU Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.072505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053331 restraints weight = 50857.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055069 restraints weight = 31129.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056220 restraints weight = 22878.383| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13568 Z= 0.159 Angle : 0.570 12.596 18412 Z= 0.287 Chirality : 0.044 0.149 1994 Planarity : 0.003 0.044 2368 Dihedral : 4.465 30.288 1790 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.69 % Allowed : 21.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1610 helix: 0.85 (0.45), residues: 158 sheet: -0.27 (0.27), residues: 376 loop : -0.94 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.003 0.001 HIS A 21 PHE 0.015 0.001 PHE B 705 TYR 0.010 0.001 TYR A 857 ARG 0.003 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 311) hydrogen bonds : angle 5.81407 ( 840) SS BOND : bond 0.00239 ( 34) SS BOND : angle 1.14238 ( 68) covalent geometry : bond 0.00368 (13534) covalent geometry : angle 0.56663 (18344) *********************** 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 73 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 33 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7953 (mmt) cc_final: 0.7359 (mmt) REVERT: A 61 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9160 (tt) REVERT: A 882 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8451 (tpm170) REVERT: B 38 MET cc_start: 0.7977 (mmt) cc_final: 0.7383 (mmt) REVERT: B 61 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9176 (tt) REVERT: B 882 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8120 (tpt90) outliers start: 40 outliers final: 27 residues processed: 71 average time/residue: 0.2450 time to fit residues: 27.2671 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 : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 158 ILE 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 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 61 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 422 THR 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 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 81 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.072406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.054130 restraints weight = 50420.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056546 restraints weight = 30329.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056737 restraints weight = 20965.560| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2021 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= 0.145 Angle : 0.576 12.298 18412 Z= 0.288 Chirality : 0.044 0.144 1994 Planarity : 0.003 0.044 2368 Dihedral : 4.457 29.474 1790 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.52 % Favored : 93.35 % Rotamer: Outliers : 2.42 % Allowed : 22.01 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1610 helix: 0.86 (0.45), residues: 158 sheet: -0.24 (0.26), residues: 376 loop : -0.90 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.003 0.001 HIS A 21 PHE 0.014 0.001 PHE B 705 TYR 0.010 0.001 TYR A 507 ARG 0.003 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 311) hydrogen bonds : angle 5.78777 ( 840) SS BOND : bond 0.00215 ( 34) SS BOND : angle 1.13846 ( 68) covalent geometry : bond 0.00337 (13534) covalent geometry : angle 0.57339 (18344) *********************** 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 70 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 34 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7960 (mmt) cc_final: 0.7371 (mmt) REVERT: A 882 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8274 (tpm170) REVERT: B 38 MET cc_start: 0.8018 (mmt) cc_final: 0.7450 (mmt) REVERT: B 61 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9153 (tt) outliers start: 36 outliers final: 28 residues processed: 68 average time/residue: 0.2094 time to fit residues: 23.6381 Evaluate side-chains 61 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 31 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 158 ILE 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 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 61 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 279 ILE 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 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 802 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 64 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.072409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.054217 restraints weight = 50167.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056508 restraints weight = 31121.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.056792 restraints weight = 21540.057| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13568 Z= 0.143 Angle : 0.595 11.748 18412 Z= 0.295 Chirality : 0.044 0.143 1994 Planarity : 0.003 0.044 2368 Dihedral : 4.502 35.791 1790 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.52 % Favored : 93.35 % Rotamer: Outliers : 2.15 % Allowed : 22.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1610 helix: 0.88 (0.45), residues: 158 sheet: -0.22 (0.26), residues: 376 loop : -0.89 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 414 HIS 0.003 0.001 HIS A 21 PHE 0.014 0.001 PHE B 705 TYR 0.010 0.001 TYR A 507 ARG 0.003 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 311) hydrogen bonds : angle 5.71688 ( 840) SS BOND : bond 0.00216 ( 34) SS BOND : angle 1.69549 ( 68) covalent geometry : bond 0.00336 (13534) covalent geometry : angle 0.58724 (18344) *********************** 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 64 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 32 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7970 (mmt) cc_final: 0.7366 (mmt) REVERT: A 61 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9129 (tt) REVERT: B 38 MET cc_start: 0.8035 (mmt) cc_final: 0.7455 (mmt) REVERT: B 61 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9162 (tt) outliers start: 32 outliers final: 27 residues processed: 62 average time/residue: 0.2356 time to fit residues: 25.6766 Evaluate side-chains 60 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 31 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 158 ILE 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 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 61 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN B 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051631 restraints weight = 50923.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053276 restraints weight = 31629.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054365 restraints weight = 23530.887| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 13568 Z= 0.280 Angle : 0.700 12.945 18412 Z= 0.347 Chirality : 0.047 0.181 1994 Planarity : 0.004 0.043 2368 Dihedral : 4.923 38.202 1790 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.70 % Favored : 92.17 % Rotamer: Outliers : 2.56 % Allowed : 21.80 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1610 helix: 0.96 (0.46), residues: 158 sheet: -0.34 (0.26), residues: 376 loop : -0.95 (0.21), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 414 HIS 0.003 0.001 HIS A 280 PHE 0.020 0.002 PHE B 705 TYR 0.011 0.001 TYR A 857 ARG 0.005 0.001 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 311) hydrogen bonds : angle 5.99706 ( 840) SS BOND : bond 0.00501 ( 34) SS BOND : angle 1.96829 ( 68) covalent geometry : bond 0.00636 (13534) covalent geometry : angle 0.69105 (18344) ********************** 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 73 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 35 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8119 (mmt) cc_final: 0.7508 (mmt) REVERT: A 61 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8776 (tt) REVERT: A 882 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8434 (tpm170) REVERT: B 38 MET cc_start: 0.8112 (mmt) cc_final: 0.7490 (mmt) REVERT: B 61 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8788 (tt) outliers start: 38 outliers final: 27 residues processed: 71 average time/residue: 0.2111 time to fit residues: 24.9316 Evaluate side-chains 62 residues out of total 1486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 32 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 158 ILE 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 585 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 802 THR 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 61 LEU 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 320 THR Chi-restraints excluded: chain B residue 422 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 HIS 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 = 0.072257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.053836 restraints weight = 50929.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055808 restraints weight = 30402.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056579 restraints weight = 21953.349| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13568 Z= 0.127 Angle : 0.643 14.427 18412 Z= 0.316 Chirality : 0.045 0.189 1994 Planarity : 0.003 0.045 2368 Dihedral : 4.701 35.241 1790 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.22 % Rotamer: Outliers : 2.02 % Allowed : 22.01 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1610 helix: 0.82 (0.45), residues: 158 sheet: -0.30 (0.26), residues: 376 loop : -0.90 (0.21), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 414 HIS 0.006 0.001 HIS B 440 PHE 0.014 0.001 PHE B 705 TYR 0.012 0.001 TYR A 507 ARG 0.004 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 311) hydrogen bonds : angle 5.78050 ( 840) SS BOND : bond 0.00264 ( 34) SS BOND : angle 1.92390 ( 68) covalent geometry : bond 0.00301 (13534) covalent geometry : angle 0.63348 (18344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3740.95 seconds wall clock time: 66 minutes 17.51 seconds (3977.51 seconds total)