Starting phenix.real_space_refine on Wed Mar 4 05:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pxw_20523/03_2026/6pxw_20523.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pxw_20523/03_2026/6pxw_20523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pxw_20523/03_2026/6pxw_20523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pxw_20523/03_2026/6pxw_20523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pxw_20523/03_2026/6pxw_20523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pxw_20523/03_2026/6pxw_20523.map" } resolution = 3.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 7116 2.51 5 N 1912 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4876 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 571} Chain breaks: 4 Chain: "B" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4876 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 571} Chain breaks: 4 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "E" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "F" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Time building chain proxies: 2.59, per 1000 atoms: 0.23 Number of scatterers: 11198 At special positions: 0 Unit cell: (129.47, 129.47, 87.74, 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 106 16.00 O 2064 8.00 N 1912 7.00 C 7116 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 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=2.02 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=2.04 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=2.04 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=2.02 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 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=2.02 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=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.04 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.02 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.04 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.02 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.02 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.04 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.02 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " 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: 0.70 Conformation dependent library (CDL) restraints added in 413.5 milliseconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 22 sheets defined 21.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.904A 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: 3.849A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.758A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.666A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.059A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.422A 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 692 through 714 removed outlier: 3.610A pdb=" N SER A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 4.080A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.904A 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: 3.850A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.757A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.665A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 4.060A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.422A 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 692 through 714 removed outlier: 3.611A pdb=" N SER B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 703 " --> pdb=" O SER B 699 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 714 " --> pdb=" O HIS B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.639A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN E 73 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 67 through 73 removed outlier: 3.640A pdb=" N LEU F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.330A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.330A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.703A pdb=" N THR A 172 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254 removed outlier: 6.864A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.388A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.585A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.520A pdb=" N ILE A 534 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.331A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 9 through 14 removed outlier: 6.331A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 64 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN B 148 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS B 121 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.703A pdb=" N THR B 172 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AB7, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.863A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC1, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.389A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC3, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.585A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.520A pdb=" N ILE B 534 " --> pdb=" O PHE B 503 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3533 1.34 - 1.46: 2575 1.46 - 1.58: 5226 1.58 - 1.70: 0 1.70 - 1.83: 124 Bond restraints: 11458 Sorted by residual: bond pdb=" C ILE B 285 " pdb=" N PRO B 286 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.30e-02 5.92e+03 4.97e+00 bond pdb=" C ILE A 285 " pdb=" N PRO A 286 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.30e-02 5.92e+03 4.63e+00 bond pdb=" CG1 ILE A 95 " pdb=" CD1 ILE A 95 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 bond pdb=" CG1 ILE B 95 " pdb=" CD1 ILE B 95 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 bond pdb=" CB VAL B 179 " pdb=" CG2 VAL B 179 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 ... (remaining 11453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 14894 2.25 - 4.50: 532 4.50 - 6.74: 69 6.74 - 8.99: 12 8.99 - 11.24: 3 Bond angle restraints: 15510 Sorted by residual: angle pdb=" C THR B 578 " pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" N HIS F 10 " pdb=" CA HIS F 10 " pdb=" C HIS F 10 " ideal model delta sigma weight residual 111.07 104.96 6.11 1.07e+00 8.73e-01 3.26e+01 angle pdb=" N HIS E 10 " pdb=" CA HIS E 10 " pdb=" C HIS E 10 " ideal model delta sigma weight residual 111.07 105.19 5.88 1.07e+00 8.73e-01 3.02e+01 angle pdb=" C GLU B 469 " pdb=" N ASN B 470 " pdb=" CA ASN B 470 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C GLU A 469 " pdb=" N ASN A 470 " pdb=" CA ASN A 470 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 ... (remaining 15505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.02: 6224 12.02 - 24.04: 550 24.04 - 36.06: 101 36.06 - 48.08: 43 48.08 - 60.10: 26 Dihedral angle restraints: 6944 sinusoidal: 2902 harmonic: 4042 Sorted by residual: dihedral pdb=" CA THR B 578 " pdb=" C THR B 578 " pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta harmonic sigma weight residual 180.00 137.11 42.89 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 149.03 -56.03 1 1.00e+01 1.00e-02 4.24e+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 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1186 0.056 - 0.112: 383 0.112 - 0.168: 106 0.168 - 0.224: 9 0.224 - 0.279: 8 Chirality restraints: 1692 Sorted by residual: chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 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 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE A 395 " pdb=" CA ILE A 395 " pdb=" CG1 ILE A 395 " pdb=" CG2 ILE A 395 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1689 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 578 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C THR B 578 " -0.050 2.00e-02 2.50e+03 pdb=" O THR B 578 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR B 579 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 542 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A 543 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 542 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO B 543 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.036 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2474 2.78 - 3.31: 9097 3.31 - 3.84: 17401 3.84 - 4.37: 20428 4.37 - 4.90: 36084 Nonbonded interactions: 85484 Sorted by model distance: nonbonded pdb=" OE2 GLU A 698 " pdb=" OH TYR B 144 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU B 698 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.295 3.040 nonbonded pdb=" OE2 GLU B 355 " pdb=" NH2 ARG B 383 " model vdw 2.334 3.120 ... (remaining 85479 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' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'D' and (resid 4 through 26 or resid 56 through 76)) selection = 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.710 Find NCS groups from input model: 0.170 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.008 0.074 11498 Z= 0.360 Angle : 0.996 11.238 15590 Z= 0.556 Chirality : 0.060 0.279 1692 Planarity : 0.007 0.066 1994 Dihedral : 9.829 58.761 4216 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.85 % Favored : 89.63 % Rotamer: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.04 (0.18), residues: 1350 helix: -3.24 (0.25), residues: 224 sheet: -2.94 (0.28), residues: 174 loop : -2.66 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 554 TYR 0.032 0.003 TYR B 579 PHE 0.025 0.004 PHE A 565 TRP 0.017 0.003 TRP A 414 HIS 0.015 0.003 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00846 (11458) covalent geometry : angle 0.99239 (15510) SS BOND : bond 0.00539 ( 40) SS BOND : angle 1.54152 ( 80) hydrogen bonds : bond 0.21433 ( 228) hydrogen bonds : angle 8.56370 ( 600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6893 (mtm-85) REVERT: B 42 ARG cc_start: 0.7404 (mmm160) cc_final: 0.6920 (mtm-85) REVERT: D 15 LEU cc_start: 0.8572 (mt) cc_final: 0.8365 (mt) REVERT: F 70 GLN cc_start: 0.8138 (mp-120) cc_final: 0.7832 (mt0) outliers start: 2 outliers final: 2 residues processed: 215 average time/residue: 0.1462 time to fit residues: 40.5173 Evaluate side-chains 104 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0030 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 32 HIS A 100 HIS A 175 ASN A 209 HIS A 247 HIS A 328 GLN A 357 ASN A 405 ASN A 407 ASN A 546 GLN A 561 GLN B 15 ASN B 32 HIS B 100 HIS B 175 ASN B 209 HIS B 247 HIS B 328 GLN B 405 ASN B 407 ASN B 429 HIS B 546 GLN B 561 GLN D 70 GLN F 70 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.093196 restraints weight = 18820.792| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.79 r_work: 0.3166 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11498 Z= 0.127 Angle : 0.617 8.599 15590 Z= 0.327 Chirality : 0.045 0.200 1692 Planarity : 0.005 0.052 1994 Dihedral : 6.045 32.620 1508 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.19 % Rotamer: Outliers : 0.63 % Allowed : 6.23 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.37 (0.20), residues: 1350 helix: -1.99 (0.29), residues: 252 sheet: -2.19 (0.36), residues: 140 loop : -2.49 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 47 TYR 0.013 0.001 TYR E 74 PHE 0.013 0.001 PHE B 565 TRP 0.007 0.001 TRP A 489 HIS 0.004 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00294 (11458) covalent geometry : angle 0.61109 (15510) SS BOND : bond 0.00296 ( 40) SS BOND : angle 1.36767 ( 80) hydrogen bonds : bond 0.03820 ( 228) hydrogen bonds : angle 6.35283 ( 600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6746 (mtm-85) REVERT: A 47 ARG cc_start: 0.7243 (mtm110) cc_final: 0.6880 (mmp-170) REVERT: A 138 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8281 (t0) REVERT: A 589 GLN cc_start: 0.7731 (pt0) cc_final: 0.7496 (tt0) REVERT: B 42 ARG cc_start: 0.7595 (mmm160) cc_final: 0.6729 (mtm-85) REVERT: B 47 ARG cc_start: 0.7255 (mtm110) cc_final: 0.6909 (mmp-170) REVERT: B 371 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7967 (ttp80) REVERT: B 589 GLN cc_start: 0.7656 (pt0) cc_final: 0.7410 (tt0) REVERT: C 72 GLU cc_start: 0.8196 (tp30) cc_final: 0.7906 (tp30) REVERT: F 60 GLN cc_start: 0.5628 (mt0) cc_final: 0.5066 (pt0) REVERT: F 70 GLN cc_start: 0.8277 (mp10) cc_final: 0.7676 (mt0) outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 0.1129 time to fit residues: 17.9693 Evaluate side-chains 95 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 290 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 295 ASN A 429 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 280 HIS B 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.116836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089107 restraints weight = 18969.675| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.85 r_work: 0.3086 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11498 Z= 0.224 Angle : 0.662 7.291 15590 Z= 0.346 Chirality : 0.047 0.154 1692 Planarity : 0.005 0.051 1994 Dihedral : 5.912 40.422 1508 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.56 % Favored : 90.37 % Rotamer: Outliers : 1.42 % Allowed : 7.26 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.07 (0.21), residues: 1350 helix: -1.52 (0.31), residues: 252 sheet: -2.10 (0.37), residues: 140 loop : -2.33 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 47 TYR 0.021 0.002 TYR B 401 PHE 0.016 0.002 PHE B 565 TRP 0.008 0.001 TRP B 489 HIS 0.006 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00541 (11458) covalent geometry : angle 0.65839 (15510) SS BOND : bond 0.00376 ( 40) SS BOND : angle 1.12715 ( 80) hydrogen bonds : bond 0.04629 ( 228) hydrogen bonds : angle 6.11216 ( 600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7584 (mmm160) cc_final: 0.6774 (mtm-85) REVERT: A 47 ARG cc_start: 0.7272 (mtm110) cc_final: 0.6874 (mmp-170) REVERT: A 138 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8072 (t0) REVERT: A 218 GLN cc_start: 0.7413 (mt0) cc_final: 0.6833 (tt0) REVERT: A 546 GLN cc_start: 0.7724 (tp40) cc_final: 0.7452 (tp-100) REVERT: B 42 ARG cc_start: 0.7621 (mmm160) cc_final: 0.6805 (mtm-85) REVERT: B 47 ARG cc_start: 0.7278 (mtm110) cc_final: 0.6885 (mmp-170) REVERT: B 218 GLN cc_start: 0.7429 (mt0) cc_final: 0.6861 (tt0) REVERT: B 371 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.8102 (ttp80) REVERT: B 546 GLN cc_start: 0.7775 (tp40) cc_final: 0.7469 (tp-100) REVERT: F 60 GLN cc_start: 0.5712 (mt0) cc_final: 0.5297 (pt0) outliers start: 18 outliers final: 6 residues processed: 107 average time/residue: 0.1230 time to fit residues: 18.3700 Evaluate side-chains 86 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 590 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 53 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 513 GLN A 561 GLN B 452 GLN B 513 GLN B 561 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.118306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090452 restraints weight = 19064.651| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.79 r_work: 0.3119 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11498 Z= 0.148 Angle : 0.577 7.241 15590 Z= 0.305 Chirality : 0.045 0.137 1692 Planarity : 0.004 0.048 1994 Dihedral : 5.559 37.132 1508 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 1.10 % Allowed : 8.28 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.74 (0.21), residues: 1350 helix: -1.15 (0.32), residues: 248 sheet: -1.92 (0.39), residues: 140 loop : -2.13 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.014 0.001 TYR B 401 PHE 0.012 0.001 PHE A 565 TRP 0.010 0.001 TRP A 412 HIS 0.004 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00357 (11458) covalent geometry : angle 0.57394 (15510) SS BOND : bond 0.00334 ( 40) SS BOND : angle 1.03723 ( 80) hydrogen bonds : bond 0.03602 ( 228) hydrogen bonds : angle 5.89719 ( 600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6777 (mtm-85) REVERT: A 47 ARG cc_start: 0.7201 (mtm110) cc_final: 0.6705 (mmp-170) REVERT: A 138 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8063 (t0) REVERT: A 546 GLN cc_start: 0.7671 (tp40) cc_final: 0.7331 (tp-100) REVERT: B 42 ARG cc_start: 0.7564 (mmm160) cc_final: 0.6801 (mtm-85) REVERT: B 47 ARG cc_start: 0.7205 (mtm110) cc_final: 0.6726 (mmp-170) REVERT: B 218 GLN cc_start: 0.7404 (mt0) cc_final: 0.6824 (tt0) REVERT: B 371 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.8022 (ttp80) REVERT: B 546 GLN cc_start: 0.7685 (tp40) cc_final: 0.7334 (tp-100) REVERT: B 554 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7692 (pmm150) outliers start: 14 outliers final: 5 residues processed: 103 average time/residue: 0.1420 time to fit residues: 19.6063 Evaluate side-chains 93 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain D residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN B 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.118549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.091541 restraints weight = 18792.080| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.72 r_work: 0.3117 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11498 Z= 0.124 Angle : 0.541 7.041 15590 Z= 0.288 Chirality : 0.043 0.135 1692 Planarity : 0.004 0.045 1994 Dihedral : 5.280 34.319 1508 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.15 % Favored : 91.78 % Rotamer: Outliers : 1.10 % Allowed : 8.75 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.51 (0.22), residues: 1350 helix: -0.91 (0.32), residues: 248 sheet: -1.86 (0.39), residues: 140 loop : -1.97 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.012 0.001 TYR A 507 PHE 0.011 0.001 PHE B 565 TRP 0.009 0.001 TRP B 412 HIS 0.004 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00297 (11458) covalent geometry : angle 0.53934 (15510) SS BOND : bond 0.00250 ( 40) SS BOND : angle 0.85149 ( 80) hydrogen bonds : bond 0.03392 ( 228) hydrogen bonds : angle 5.72999 ( 600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7479 (mmm160) cc_final: 0.6827 (mtm-85) REVERT: A 47 ARG cc_start: 0.7181 (mtm110) cc_final: 0.6656 (mmp-170) REVERT: A 138 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8100 (t0) REVERT: A 218 GLN cc_start: 0.7392 (mt0) cc_final: 0.6793 (tt0) REVERT: A 546 GLN cc_start: 0.7690 (tp40) cc_final: 0.7408 (tp-100) REVERT: A 554 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7419 (pmm150) REVERT: B 42 ARG cc_start: 0.7489 (mmm160) cc_final: 0.6805 (mtm-85) REVERT: B 47 ARG cc_start: 0.7087 (mtm110) cc_final: 0.6614 (mmp-170) REVERT: B 218 GLN cc_start: 0.7388 (mt0) cc_final: 0.6800 (tt0) REVERT: B 371 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.8076 (ttp80) REVERT: B 546 GLN cc_start: 0.7676 (tp40) cc_final: 0.7380 (tp-100) REVERT: B 554 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7760 (pmm150) outliers start: 14 outliers final: 5 residues processed: 107 average time/residue: 0.1212 time to fit residues: 17.9871 Evaluate side-chains 91 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain D residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 546 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091781 restraints weight = 19037.304| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.81 r_work: 0.3135 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11498 Z= 0.104 Angle : 0.518 7.116 15590 Z= 0.276 Chirality : 0.043 0.135 1692 Planarity : 0.003 0.044 1994 Dihedral : 5.056 32.170 1508 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.59 % Rotamer: Outliers : 1.50 % Allowed : 9.15 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.37 (0.22), residues: 1350 helix: -0.72 (0.32), residues: 248 sheet: -1.97 (0.41), residues: 130 loop : -1.87 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 22 TYR 0.011 0.001 TYR B 507 PHE 0.011 0.001 PHE B 565 TRP 0.009 0.001 TRP B 412 HIS 0.016 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00245 (11458) covalent geometry : angle 0.51684 (15510) SS BOND : bond 0.00212 ( 40) SS BOND : angle 0.76369 ( 80) hydrogen bonds : bond 0.03144 ( 228) hydrogen bonds : angle 5.62951 ( 600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7522 (mmm160) cc_final: 0.6804 (mtm-85) REVERT: A 47 ARG cc_start: 0.7110 (mtm110) cc_final: 0.6601 (mmp-170) REVERT: A 138 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7952 (t0) REVERT: A 218 GLN cc_start: 0.7361 (mt0) cc_final: 0.6918 (mp10) REVERT: A 546 GLN cc_start: 0.7608 (tp40) cc_final: 0.7364 (tp-100) REVERT: A 554 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7363 (pmm150) REVERT: B 42 ARG cc_start: 0.7460 (mmm160) cc_final: 0.6854 (mtm-85) REVERT: B 47 ARG cc_start: 0.7123 (mtm110) cc_final: 0.6607 (mmp-170) REVERT: B 218 GLN cc_start: 0.7361 (mt0) cc_final: 0.6767 (tt0) REVERT: B 371 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.8014 (ttp80) REVERT: B 546 GLN cc_start: 0.7686 (tp-100) cc_final: 0.7394 (tp-100) REVERT: B 554 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7596 (pmm150) REVERT: C 22 ARG cc_start: 0.8399 (mtm180) cc_final: 0.8161 (ptt180) outliers start: 19 outliers final: 6 residues processed: 111 average time/residue: 0.1277 time to fit residues: 19.2748 Evaluate side-chains 95 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.119266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.091868 restraints weight = 18780.704| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.72 r_work: 0.3147 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11498 Z= 0.105 Angle : 0.511 7.049 15590 Z= 0.272 Chirality : 0.043 0.136 1692 Planarity : 0.003 0.043 1994 Dihedral : 4.952 34.365 1508 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.00 % Favored : 91.93 % Rotamer: Outliers : 1.10 % Allowed : 9.78 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.27 (0.22), residues: 1350 helix: -0.54 (0.33), residues: 248 sheet: -1.92 (0.41), residues: 130 loop : -1.83 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.013 0.001 TYR B 579 PHE 0.011 0.001 PHE A 565 TRP 0.009 0.001 TRP B 412 HIS 0.003 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00249 (11458) covalent geometry : angle 0.50930 (15510) SS BOND : bond 0.00196 ( 40) SS BOND : angle 0.78921 ( 80) hydrogen bonds : bond 0.03154 ( 228) hydrogen bonds : angle 5.60473 ( 600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6851 (mtm-85) REVERT: A 47 ARG cc_start: 0.7087 (mtm110) cc_final: 0.6592 (mmp-170) REVERT: A 138 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7941 (t0) REVERT: A 218 GLN cc_start: 0.7385 (mt0) cc_final: 0.6847 (mp10) REVERT: A 546 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7440 (tp-100) REVERT: A 554 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7398 (pmm150) REVERT: B 42 ARG cc_start: 0.7610 (mmm160) cc_final: 0.6894 (mtm-85) REVERT: B 47 ARG cc_start: 0.7047 (mtm110) cc_final: 0.6573 (mmp-170) REVERT: B 218 GLN cc_start: 0.7354 (mt0) cc_final: 0.6862 (mp10) REVERT: B 371 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.8000 (ttp80) REVERT: B 546 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7430 (tp-100) REVERT: B 554 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7611 (pmm150) outliers start: 14 outliers final: 5 residues processed: 99 average time/residue: 0.1373 time to fit residues: 18.3645 Evaluate side-chains 92 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain D residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 116 optimal weight: 0.0670 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.0060 overall best weight: 0.3534 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.120738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.093364 restraints weight = 18887.661| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.75 r_work: 0.3165 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11498 Z= 0.083 Angle : 0.487 6.760 15590 Z= 0.260 Chirality : 0.042 0.136 1692 Planarity : 0.003 0.043 1994 Dihedral : 4.766 31.384 1508 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.71 % Allowed : 10.49 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.10 (0.22), residues: 1350 helix: -0.35 (0.33), residues: 248 sheet: -1.83 (0.42), residues: 130 loop : -1.72 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 22 TYR 0.011 0.001 TYR B 579 PHE 0.010 0.001 PHE B 565 TRP 0.009 0.001 TRP B 412 HIS 0.002 0.000 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00184 (11458) covalent geometry : angle 0.48628 (15510) SS BOND : bond 0.00185 ( 40) SS BOND : angle 0.67678 ( 80) hydrogen bonds : bond 0.02892 ( 228) hydrogen bonds : angle 5.50549 ( 600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7541 (mmm160) cc_final: 0.6870 (mtm-85) REVERT: A 47 ARG cc_start: 0.7071 (mtm110) cc_final: 0.6597 (mmp-170) REVERT: A 138 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8022 (t0) REVERT: A 218 GLN cc_start: 0.7299 (mt0) cc_final: 0.6798 (mp10) REVERT: A 554 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7237 (pmm150) REVERT: B 42 ARG cc_start: 0.7553 (mmm160) cc_final: 0.6893 (mtm-85) REVERT: B 218 GLN cc_start: 0.7314 (mt0) cc_final: 0.6823 (mp10) REVERT: B 371 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.7989 (ttp80) outliers start: 9 outliers final: 1 residues processed: 98 average time/residue: 0.1291 time to fit residues: 17.6533 Evaluate side-chains 88 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.0570 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 51 optimal weight: 0.0050 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 overall best weight: 0.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN B 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.120978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.093770 restraints weight = 18741.789| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.71 r_work: 0.3174 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11498 Z= 0.086 Angle : 0.488 7.128 15590 Z= 0.259 Chirality : 0.042 0.135 1692 Planarity : 0.003 0.041 1994 Dihedral : 4.606 30.535 1507 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.71 % Allowed : 10.57 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.02 (0.22), residues: 1350 helix: -0.24 (0.34), residues: 248 sheet: -1.80 (0.42), residues: 130 loop : -1.68 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 47 TYR 0.011 0.001 TYR B 579 PHE 0.010 0.001 PHE B 565 TRP 0.011 0.001 TRP B 493 HIS 0.005 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00196 (11458) covalent geometry : angle 0.48749 (15510) SS BOND : bond 0.00168 ( 40) SS BOND : angle 0.64767 ( 80) hydrogen bonds : bond 0.02890 ( 228) hydrogen bonds : angle 5.49138 ( 600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7536 (mmm160) cc_final: 0.6883 (mtm-85) REVERT: A 138 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.8007 (t0) REVERT: A 218 GLN cc_start: 0.7281 (mt0) cc_final: 0.6780 (mp10) REVERT: A 554 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7325 (pmm150) REVERT: B 42 ARG cc_start: 0.7541 (mmm160) cc_final: 0.6902 (mtm-85) REVERT: B 371 ARG cc_start: 0.8258 (ttp-170) cc_final: 0.7995 (ttp80) REVERT: C 22 ARG cc_start: 0.8292 (ptt180) cc_final: 0.8075 (ptt180) outliers start: 9 outliers final: 3 residues processed: 98 average time/residue: 0.1208 time to fit residues: 16.5284 Evaluate side-chains 91 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.0670 chunk 134 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN B 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.120868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.093512 restraints weight = 18893.041| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.74 r_work: 0.3171 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11498 Z= 0.095 Angle : 0.504 7.387 15590 Z= 0.266 Chirality : 0.042 0.132 1692 Planarity : 0.003 0.042 1994 Dihedral : 4.577 30.480 1507 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.39 % Allowed : 11.20 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.22), residues: 1350 helix: -0.23 (0.34), residues: 250 sheet: -1.80 (0.42), residues: 130 loop : -1.66 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 47 TYR 0.012 0.001 TYR B 579 PHE 0.010 0.001 PHE A 565 TRP 0.008 0.001 TRP B 412 HIS 0.004 0.001 HIS E 5 Details of bonding type rmsd covalent geometry : bond 0.00219 (11458) covalent geometry : angle 0.50195 (15510) SS BOND : bond 0.00201 ( 40) SS BOND : angle 0.79598 ( 80) hydrogen bonds : bond 0.02949 ( 228) hydrogen bonds : angle 5.54907 ( 600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7524 (mmm160) cc_final: 0.6863 (mtm-85) REVERT: A 138 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7793 (t0) REVERT: A 218 GLN cc_start: 0.7256 (mt0) cc_final: 0.6734 (mp10) REVERT: A 554 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7319 (pmm150) REVERT: B 42 ARG cc_start: 0.7501 (mmm160) cc_final: 0.6872 (mtm-85) REVERT: B 218 GLN cc_start: 0.7280 (mt0) cc_final: 0.6745 (mp10) REVERT: B 371 ARG cc_start: 0.8260 (ttp-170) cc_final: 0.7982 (ttp80) REVERT: C 22 ARG cc_start: 0.8338 (ptt180) cc_final: 0.8132 (ptt180) outliers start: 5 outliers final: 3 residues processed: 95 average time/residue: 0.1254 time to fit residues: 16.7147 Evaluate side-chains 89 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 63 optimal weight: 0.6980 chunk 114 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 121 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.122356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095080 restraints weight = 18801.163| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.72 r_work: 0.3195 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11498 Z= 0.083 Angle : 0.492 7.263 15590 Z= 0.259 Chirality : 0.042 0.134 1692 Planarity : 0.003 0.043 1994 Dihedral : 4.428 29.775 1507 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.39 % Allowed : 11.36 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.22), residues: 1350 helix: -0.13 (0.33), residues: 250 sheet: -1.76 (0.42), residues: 130 loop : -1.61 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 22 TYR 0.009 0.001 TYR A 507 PHE 0.009 0.001 PHE B 565 TRP 0.009 0.001 TRP B 412 HIS 0.005 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00186 (11458) covalent geometry : angle 0.49022 (15510) SS BOND : bond 0.00152 ( 40) SS BOND : angle 0.77029 ( 80) hydrogen bonds : bond 0.02796 ( 228) hydrogen bonds : angle 5.46568 ( 600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.87 seconds wall clock time: 40 minutes 6.81 seconds (2406.81 seconds total)