Starting phenix.real_space_refine on Wed Mar 4 22:22:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl3_25190/03_2026/7sl3_25190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl3_25190/03_2026/7sl3_25190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sl3_25190/03_2026/7sl3_25190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl3_25190/03_2026/7sl3_25190.map" model { file = "/net/cci-nas-00/data/ceres_data/7sl3_25190/03_2026/7sl3_25190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl3_25190/03_2026/7sl3_25190_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 3460 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 112 5.16 5 C 8898 2.51 5 N 2408 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14016 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "B" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "D" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "E" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 3.16, per 1000 atoms: 0.23 Number of scatterers: 14016 At special positions: 0 Unit cell: (139.32, 115.56, 174.96, 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 112 16.00 O 2598 8.00 N 2408 7.00 C 8898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 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 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 465.5 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 17.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.977A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 24' Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.733A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.817A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.593A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.801A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.695A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.521A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.502A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' 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 640 through 645 removed outlier: 3.962A pdb=" N PHE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 645' Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 18 through 24 removed outlier: 4.066A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 24' Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.719A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.837A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.584A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.807A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.686A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.511A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.506A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' 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 640 through 645 removed outlier: 4.028A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 690 through 716 removed outlier: 5.283A pdb=" N LYS B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.768A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.745A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.536A pdb=" N GLU E 17 " --> pdb=" O TYR E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.502A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.844A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.550A pdb=" N LEU A 368 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.772A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.619A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 601 through 607 removed outlier: 5.897A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 770 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.045A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 630 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 762 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.045A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 824 removed outlier: 3.553A pdb=" N VAL A 830 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 858 through 864 removed outlier: 6.896A pdb=" N THR A 891 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 847 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 889 " --> pdb=" O TYR A 847 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 849 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A 887 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 851 " --> pdb=" O SER A 885 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 885 " --> pdb=" O TYR A 851 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A 853 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN A 883 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.598A pdb=" N LEU B 36 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.840A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.580A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.718A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC7, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC9, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.543A pdb=" N LEU B 368 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD2, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.735A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.548A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.599A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.509A pdb=" N GLU B 762 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD7, first strand: chain 'B' and resid 858 through 864 removed outlier: 6.847A pdb=" N THR B 891 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 847 " --> pdb=" O ARG B 889 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 889 " --> pdb=" O TYR B 847 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 849 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 887 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR B 851 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER B 885 " --> pdb=" O TYR B 851 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG B 853 " --> pdb=" O ASN B 883 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN B 883 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4591 1.34 - 1.46: 3333 1.46 - 1.58: 6298 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14358 Sorted by residual: bond pdb=" CA THR B 690 " pdb=" CB THR B 690 " ideal model delta sigma weight residual 1.518 1.540 -0.023 2.08e-02 2.31e+03 1.18e+00 bond pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CA LYS B 559 " pdb=" CB LYS B 559 " ideal model delta sigma weight residual 1.519 1.537 -0.017 1.73e-02 3.34e+03 9.81e-01 bond pdb=" CA CYS B 687 " pdb=" C CYS B 687 " ideal model delta sigma weight residual 1.524 1.516 0.008 8.10e-03 1.52e+04 9.47e-01 bond pdb=" CA LYS A 559 " pdb=" CB LYS A 559 " ideal model delta sigma weight residual 1.519 1.536 -0.016 1.73e-02 3.34e+03 9.03e-01 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 19248 2.20 - 4.40: 198 4.40 - 6.59: 11 6.59 - 8.79: 1 8.79 - 10.99: 2 Bond angle restraints: 19460 Sorted by residual: angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 132.53 -10.99 1.91e+00 2.74e-01 3.31e+01 angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C THR B 690 " pdb=" CA THR B 690 " pdb=" CB THR B 690 " ideal model delta sigma weight residual 115.79 109.56 6.23 1.19e+00 7.06e-01 2.74e+01 angle pdb=" N ASP A 691 " pdb=" CA ASP A 691 " pdb=" C ASP A 691 " ideal model delta sigma weight residual 113.41 109.26 4.15 1.22e+00 6.72e-01 1.16e+01 angle pdb=" N SER B 692 " pdb=" CA SER B 692 " pdb=" C SER B 692 " ideal model delta sigma weight residual 113.19 109.62 3.57 1.19e+00 7.06e-01 8.98e+00 ... (remaining 19455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7931 17.94 - 35.87: 628 35.87 - 53.81: 114 53.81 - 71.74: 29 71.74 - 89.68: 10 Dihedral angle restraints: 8712 sinusoidal: 3640 harmonic: 5072 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -148.27 62.27 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -147.43 61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 147.12 -54.12 1 1.00e+01 1.00e-02 3.97e+01 ... (remaining 8709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1357 0.034 - 0.068: 490 0.068 - 0.101: 164 0.101 - 0.135: 95 0.135 - 0.169: 4 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB THR A 690 " pdb=" CA THR A 690 " pdb=" OG1 THR A 690 " pdb=" CG2 THR A 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 2107 not shown) Planarity restraints: 2516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C THR B 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C THR A 580 " -0.039 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 836 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 837 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 837 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 837 " 0.017 5.00e-02 4.00e+02 ... (remaining 2513 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2332 2.77 - 3.30: 13128 3.30 - 3.84: 22468 3.84 - 4.37: 26556 4.37 - 4.90: 45564 Nonbonded interactions: 110048 Sorted by model distance: nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.238 3.040 nonbonded pdb=" NH2 ARG A 14 " pdb=" O VAL B 715 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 715 " pdb=" NH2 ARG B 14 " model vdw 2.245 3.120 nonbonded pdb=" NE2 GLN A 790 " pdb=" O ASP A 794 " model vdw 2.246 3.120 ... (remaining 110043 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.690 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.002 0.039 14398 Z= 0.111 Angle : 0.539 10.991 19540 Z= 0.288 Chirality : 0.043 0.169 2110 Planarity : 0.003 0.031 2516 Dihedral : 13.247 89.680 5316 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.35 % Favored : 93.41 % Rotamer: Outliers : 0.32 % Allowed : 0.32 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1700 helix: -0.32 (0.36), residues: 222 sheet: 0.84 (0.30), residues: 334 loop : -0.95 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 578 TYR 0.014 0.001 TYR B 581 PHE 0.013 0.001 PHE B 778 TRP 0.009 0.001 TRP A 412 HIS 0.003 0.000 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00239 (14358) covalent geometry : angle 0.53683 (19460) SS BOND : bond 0.00193 ( 40) SS BOND : angle 0.97940 ( 80) hydrogen bonds : bond 0.23714 ( 333) hydrogen bonds : angle 8.15140 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: B 687 CYS cc_start: 0.2703 (OUTLIER) cc_final: 0.2494 (m) REVERT: F 17 GLU cc_start: 0.7541 (mp0) cc_final: 0.7209 (mp0) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.1111 time to fit residues: 12.6334 Evaluate side-chains 55 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 689 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 452 GLN B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 452 GLN B 712 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.103094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069452 restraints weight = 40046.612| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.37 r_work: 0.3112 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14398 Z= 0.166 Angle : 0.554 6.642 19540 Z= 0.291 Chirality : 0.045 0.196 2110 Planarity : 0.003 0.032 2516 Dihedral : 4.942 54.321 1905 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.06 % Favored : 93.76 % Rotamer: Outliers : 0.25 % Allowed : 5.06 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.21), residues: 1700 helix: 0.34 (0.37), residues: 212 sheet: 0.86 (0.30), residues: 332 loop : -0.97 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 782 TYR 0.015 0.001 TYR E 14 PHE 0.012 0.001 PHE A 381 TRP 0.008 0.001 TRP A 412 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00394 (14358) covalent geometry : angle 0.55247 (19460) SS BOND : bond 0.00551 ( 40) SS BOND : angle 0.82745 ( 80) hydrogen bonds : bond 0.04934 ( 333) hydrogen bonds : angle 6.16685 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 691 ASP cc_start: 0.8124 (p0) cc_final: 0.7675 (p0) REVERT: A 808 MET cc_start: 0.6057 (ptt) cc_final: 0.5747 (mmp) REVERT: E 14 TYR cc_start: 0.8080 (t80) cc_final: 0.7653 (t80) REVERT: E 17 GLU cc_start: 0.7840 (mp0) cc_final: 0.7462 (mp0) REVERT: F 14 TYR cc_start: 0.7957 (t80) cc_final: 0.7311 (t80) REVERT: F 17 GLU cc_start: 0.8139 (mp0) cc_final: 0.7619 (mp0) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 0.0997 time to fit residues: 9.9883 Evaluate side-chains 52 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 0 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.0770 chunk 140 optimal weight: 2.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.103304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069800 restraints weight = 40766.547| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.41 r_work: 0.3112 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14398 Z= 0.129 Angle : 0.514 7.332 19540 Z= 0.270 Chirality : 0.044 0.187 2110 Planarity : 0.003 0.033 2516 Dihedral : 4.638 34.517 1900 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.06 % Rotamer: Outliers : 0.32 % Allowed : 7.71 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1700 helix: 0.60 (0.38), residues: 210 sheet: 0.59 (0.30), residues: 342 loop : -0.93 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 782 TYR 0.025 0.001 TYR B 581 PHE 0.012 0.001 PHE B 707 TRP 0.008 0.001 TRP A 412 HIS 0.004 0.001 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00307 (14358) covalent geometry : angle 0.51067 (19460) SS BOND : bond 0.00270 ( 40) SS BOND : angle 1.03400 ( 80) hydrogen bonds : bond 0.04140 ( 333) hydrogen bonds : angle 5.68710 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 691 ASP cc_start: 0.8112 (p0) cc_final: 0.7752 (p0) REVERT: A 833 MET cc_start: 0.5142 (mmt) cc_final: 0.4480 (tpt) REVERT: E 14 TYR cc_start: 0.8096 (t80) cc_final: 0.7594 (t80) REVERT: E 17 GLU cc_start: 0.7937 (mp0) cc_final: 0.7551 (mp0) REVERT: F 14 TYR cc_start: 0.7971 (t80) cc_final: 0.7327 (t80) REVERT: F 17 GLU cc_start: 0.8108 (mp0) cc_final: 0.7512 (mp0) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.1033 time to fit residues: 10.2208 Evaluate side-chains 52 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 53 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 169 optimal weight: 0.0060 chunk 13 optimal weight: 2.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.102351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.068914 restraints weight = 40616.847| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.38 r_work: 0.3091 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14398 Z= 0.160 Angle : 0.530 7.724 19540 Z= 0.278 Chirality : 0.044 0.207 2110 Planarity : 0.003 0.033 2516 Dihedral : 4.752 33.584 1900 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 0.76 % Allowed : 9.54 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1700 helix: 0.55 (0.38), residues: 210 sheet: 0.48 (0.29), residues: 346 loop : -0.97 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 636 TYR 0.024 0.001 TYR B 581 PHE 0.011 0.001 PHE A 778 TRP 0.007 0.001 TRP B 412 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00382 (14358) covalent geometry : angle 0.52678 (19460) SS BOND : bond 0.00276 ( 40) SS BOND : angle 1.06206 ( 80) hydrogen bonds : bond 0.03957 ( 333) hydrogen bonds : angle 5.53719 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 691 ASP cc_start: 0.8071 (p0) cc_final: 0.7661 (p0) REVERT: A 833 MET cc_start: 0.5070 (mmt) cc_final: 0.4422 (tpt) REVERT: E 14 TYR cc_start: 0.8166 (t80) cc_final: 0.7747 (t80) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.0994 time to fit residues: 11.0667 Evaluate side-chains 55 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 70 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.102895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.069318 restraints weight = 40112.549| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.43 r_work: 0.3119 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14398 Z= 0.130 Angle : 0.513 6.083 19540 Z= 0.269 Chirality : 0.044 0.226 2110 Planarity : 0.003 0.033 2516 Dihedral : 4.640 33.506 1900 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.70 % Allowed : 10.68 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1700 helix: 0.57 (0.38), residues: 210 sheet: 0.56 (0.29), residues: 342 loop : -0.98 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 782 TYR 0.024 0.001 TYR B 581 PHE 0.011 0.001 PHE A 707 TRP 0.007 0.001 TRP A 412 HIS 0.004 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00312 (14358) covalent geometry : angle 0.51174 (19460) SS BOND : bond 0.00237 ( 40) SS BOND : angle 0.73581 ( 80) hydrogen bonds : bond 0.03758 ( 333) hydrogen bonds : angle 5.37992 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 691 ASP cc_start: 0.8060 (p0) cc_final: 0.7652 (p0) REVERT: A 833 MET cc_start: 0.5334 (mmt) cc_final: 0.4586 (tpt) REVERT: B 98 MET cc_start: 0.9071 (mmm) cc_final: 0.8483 (tpt) REVERT: B 120 GLU cc_start: 0.8224 (tt0) cc_final: 0.8012 (tt0) REVERT: E 17 GLU cc_start: 0.7756 (mp0) cc_final: 0.7514 (pm20) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.1026 time to fit residues: 10.9191 Evaluate side-chains 58 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 1 optimal weight: 0.0070 chunk 76 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 0.0070 chunk 104 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.102998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069477 restraints weight = 40211.992| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.44 r_work: 0.3122 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14398 Z= 0.118 Angle : 0.504 6.314 19540 Z= 0.264 Chirality : 0.043 0.215 2110 Planarity : 0.003 0.032 2516 Dihedral : 4.547 33.925 1900 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 0.70 % Allowed : 11.00 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1700 helix: 0.55 (0.38), residues: 210 sheet: 0.60 (0.29), residues: 342 loop : -0.95 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 22 TYR 0.022 0.001 TYR B 581 PHE 0.011 0.001 PHE A 707 TRP 0.007 0.001 TRP A 412 HIS 0.003 0.001 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00284 (14358) covalent geometry : angle 0.50312 (19460) SS BOND : bond 0.00232 ( 40) SS BOND : angle 0.64983 ( 80) hydrogen bonds : bond 0.03580 ( 333) hydrogen bonds : angle 5.25789 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 691 ASP cc_start: 0.8038 (p0) cc_final: 0.7707 (p0) REVERT: B 98 MET cc_start: 0.9118 (mmm) cc_final: 0.8642 (tpt) REVERT: B 344 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8921 (mp) REVERT: B 782 ARG cc_start: 0.9159 (mmm-85) cc_final: 0.8707 (mmm-85) REVERT: C 21 GLU cc_start: 0.7068 (pm20) cc_final: 0.6560 (pp20) REVERT: E 17 GLU cc_start: 0.7870 (mp0) cc_final: 0.7603 (pm20) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.1038 time to fit residues: 10.9243 Evaluate side-chains 61 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 100 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 170 optimal weight: 0.0030 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.101798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.068252 restraints weight = 40282.107| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.42 r_work: 0.3080 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14398 Z= 0.184 Angle : 0.537 6.052 19540 Z= 0.281 Chirality : 0.044 0.198 2110 Planarity : 0.003 0.030 2516 Dihedral : 4.659 33.082 1900 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.63 % Allowed : 11.57 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1700 helix: 0.35 (0.37), residues: 222 sheet: 0.35 (0.29), residues: 350 loop : -0.98 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.022 0.001 TYR B 581 PHE 0.014 0.001 PHE A 778 TRP 0.007 0.001 TRP A 412 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00437 (14358) covalent geometry : angle 0.53548 (19460) SS BOND : bond 0.00286 ( 40) SS BOND : angle 0.84533 ( 80) hydrogen bonds : bond 0.03864 ( 333) hydrogen bonds : angle 5.28481 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 691 ASP cc_start: 0.8089 (p0) cc_final: 0.7741 (p0) REVERT: B 344 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8987 (mp) REVERT: E 17 GLU cc_start: 0.7864 (mp0) cc_final: 0.7586 (pm20) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.0982 time to fit residues: 9.3457 Evaluate side-chains 57 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 107 optimal weight: 0.1980 chunk 143 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.102755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069290 restraints weight = 39765.532| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.42 r_work: 0.3120 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14398 Z= 0.113 Angle : 0.502 6.633 19540 Z= 0.263 Chirality : 0.043 0.188 2110 Planarity : 0.003 0.030 2516 Dihedral : 4.538 33.679 1900 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.63 % Allowed : 11.69 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1700 helix: 0.51 (0.38), residues: 210 sheet: 0.50 (0.29), residues: 350 loop : -0.95 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.019 0.001 TYR B 581 PHE 0.013 0.001 PHE A 778 TRP 0.007 0.001 TRP A 412 HIS 0.002 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00271 (14358) covalent geometry : angle 0.50111 (19460) SS BOND : bond 0.00223 ( 40) SS BOND : angle 0.68115 ( 80) hydrogen bonds : bond 0.03487 ( 333) hydrogen bonds : angle 5.15635 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 477 PHE cc_start: 0.8611 (t80) cc_final: 0.8359 (t80) REVERT: A 691 ASP cc_start: 0.8028 (p0) cc_final: 0.7674 (p0) REVERT: B 344 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8896 (mp) REVERT: E 17 GLU cc_start: 0.7826 (mp0) cc_final: 0.7569 (pm20) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.1057 time to fit residues: 11.2531 Evaluate side-chains 60 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 134 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 61 optimal weight: 0.0870 chunk 22 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.103074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069698 restraints weight = 40185.334| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.44 r_work: 0.3131 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14398 Z= 0.101 Angle : 0.497 6.790 19540 Z= 0.260 Chirality : 0.043 0.183 2110 Planarity : 0.003 0.033 2516 Dihedral : 4.441 34.747 1900 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.70 % Allowed : 12.20 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1700 helix: 0.18 (0.37), residues: 222 sheet: 0.57 (0.29), residues: 350 loop : -0.97 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 782 TYR 0.018 0.001 TYR B 581 PHE 0.011 0.001 PHE B 707 TRP 0.008 0.001 TRP A 412 HIS 0.002 0.000 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00244 (14358) covalent geometry : angle 0.49654 (19460) SS BOND : bond 0.00207 ( 40) SS BOND : angle 0.61256 ( 80) hydrogen bonds : bond 0.03327 ( 333) hydrogen bonds : angle 5.05903 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 442 MET cc_start: 0.8950 (ttm) cc_final: 0.8162 (tpp) REVERT: A 477 PHE cc_start: 0.8590 (t80) cc_final: 0.8379 (t80) REVERT: A 691 ASP cc_start: 0.7925 (p0) cc_final: 0.7605 (p0) REVERT: B 344 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8873 (mp) REVERT: B 477 PHE cc_start: 0.8601 (t80) cc_final: 0.8377 (t80) REVERT: E 17 GLU cc_start: 0.7806 (mp0) cc_final: 0.7556 (pm20) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.0963 time to fit residues: 9.8983 Evaluate side-chains 60 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.101649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068063 restraints weight = 40297.959| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.43 r_work: 0.3091 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14398 Z= 0.174 Angle : 0.535 6.673 19540 Z= 0.279 Chirality : 0.044 0.192 2110 Planarity : 0.003 0.035 2516 Dihedral : 4.592 32.776 1900 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.63 % Allowed : 12.14 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1700 helix: 0.27 (0.37), residues: 222 sheet: 0.37 (0.29), residues: 364 loop : -0.95 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 806 TYR 0.020 0.001 TYR B 581 PHE 0.011 0.001 PHE B 381 TRP 0.008 0.001 TRP B 834 HIS 0.004 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00416 (14358) covalent geometry : angle 0.53327 (19460) SS BOND : bond 0.00279 ( 40) SS BOND : angle 0.81667 ( 80) hydrogen bonds : bond 0.03746 ( 333) hydrogen bonds : angle 5.15760 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 442 MET cc_start: 0.9033 (ttm) cc_final: 0.8123 (tpp) REVERT: A 691 ASP cc_start: 0.8022 (p0) cc_final: 0.7694 (p0) REVERT: B 344 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8930 (mp) REVERT: E 17 GLU cc_start: 0.7779 (mp0) cc_final: 0.7458 (pm20) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.0954 time to fit residues: 9.3496 Evaluate side-chains 56 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 31 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 125 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.102887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.069558 restraints weight = 40014.793| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.43 r_work: 0.3112 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14398 Z= 0.098 Angle : 0.505 6.976 19540 Z= 0.263 Chirality : 0.043 0.180 2110 Planarity : 0.003 0.036 2516 Dihedral : 4.463 34.170 1900 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.44 % Allowed : 12.58 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1700 helix: 0.20 (0.37), residues: 222 sheet: 0.42 (0.29), residues: 364 loop : -0.94 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 782 TYR 0.015 0.001 TYR B 512 PHE 0.013 0.001 PHE A 707 TRP 0.009 0.001 TRP B 412 HIS 0.002 0.000 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00233 (14358) covalent geometry : angle 0.50450 (19460) SS BOND : bond 0.00212 ( 40) SS BOND : angle 0.61261 ( 80) hydrogen bonds : bond 0.03331 ( 333) hydrogen bonds : angle 5.03654 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3319.89 seconds wall clock time: 57 minutes 30.35 seconds (3450.35 seconds total)