Starting phenix.real_space_refine on Wed Mar 4 05:03:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmj_27541/03_2026/8dmj_27541_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmj_27541/03_2026/8dmj_27541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dmj_27541/03_2026/8dmj_27541_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmj_27541/03_2026/8dmj_27541_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dmj_27541/03_2026/8dmj_27541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmj_27541/03_2026/8dmj_27541.map" } resolution = 3.2 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= 0.001 sd= 0.015 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 67 5.16 5 C 7002 2.51 5 N 1821 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 11030 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 1 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 1 Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.76, per 1000 atoms: 0.25 Number of scatterers: 11030 At special positions: 0 Unit cell: (106.11, 110.97, 157.14, 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 67 16.00 O 2140 8.00 N 1821 7.00 C 7002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 0.84 Conformation dependent library (CDL) restraints added in 536.0 milliseconds 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 24 sheets defined 25.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 72 through 93 removed outlier: 3.507A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 190 through 220 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.745A pdb=" N LYS A 362 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 74 through 93 Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 190 through 214 Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.671A pdb=" N ARG B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.720A pdb=" N LYS B 362 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.598A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 93 Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 190 through 214 Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 358 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.615A pdb=" N CYS C 363 " --> pdb=" O THR C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.719A pdb=" N LYS H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.611A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 333 removed outlier: 5.693A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 295 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 44 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 225 removed outlier: 5.924A pdb=" N VAL A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A 266 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR A 54 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER C 435 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP A 56 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASN C 437 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 58 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 437 removed outlier: 6.503A pdb=" N THR B 54 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY A 434 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 56 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 332 through 333 removed outlier: 5.898A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB2, first strand: chain 'B' and resid 431 through 437 removed outlier: 4.824A pdb=" N ASP C 56 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER B 435 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 58 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN B 437 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LYS C 60 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 332 through 333 removed outlier: 7.742A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS C 40 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU C 297 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL C 42 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C 291 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 11.554A pdb=" N ILE C 48 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 10.653A pdb=" N GLN C 289 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.868A pdb=" N GLU D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 107 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 89 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE D 34 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.868A pdb=" N GLU D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 107 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.522A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN E 50 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.079A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.982A pdb=" N GLU H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR H 107 " --> pdb=" O PHE H 90 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.560A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1266 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: 2.05 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3538 1.35 - 1.46: 2608 1.46 - 1.58: 4996 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 11238 Sorted by residual: bond pdb=" N VAL L 29 " pdb=" CA VAL L 29 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.04e-02 9.25e+03 1.20e+01 bond pdb=" N ILE B 288 " pdb=" CA ILE B 288 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.55e+00 bond pdb=" N ILE C 288 " pdb=" CA ILE C 288 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.30e-02 5.92e+03 7.93e+00 bond pdb=" N LEU C 285 " pdb=" CA LEU C 285 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.53e+00 bond pdb=" N ILE C 90 " pdb=" CA ILE C 90 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.22e+00 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 15041 2.31 - 4.62: 192 4.62 - 6.94: 10 6.94 - 9.25: 3 9.25 - 11.56: 1 Bond angle restraints: 15247 Sorted by residual: angle pdb=" CA GLN B 290 " pdb=" C GLN B 290 " pdb=" O GLN B 290 " ideal model delta sigma weight residual 121.67 117.98 3.69 9.30e-01 1.16e+00 1.57e+01 angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" C VAL L 29 " ideal model delta sigma weight residual 112.43 108.86 3.57 9.20e-01 1.18e+00 1.51e+01 angle pdb=" CA ILE B 288 " pdb=" C ILE B 288 " pdb=" O ILE B 288 " ideal model delta sigma weight residual 121.58 118.06 3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" CA ILE C 288 " pdb=" C ILE C 288 " pdb=" O ILE C 288 " ideal model delta sigma weight residual 121.58 118.06 3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" N THR L 69 " pdb=" CA THR L 69 " pdb=" C THR L 69 " ideal model delta sigma weight residual 114.56 110.30 4.26 1.27e+00 6.20e-01 1.12e+01 ... (remaining 15242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6061 17.68 - 35.36: 527 35.36 - 53.05: 162 53.05 - 70.73: 27 70.73 - 88.41: 7 Dihedral angle restraints: 6784 sinusoidal: 2665 harmonic: 4119 Sorted by residual: dihedral pdb=" CB CYS C 394 " pdb=" SG CYS C 394 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual -86.00 -150.10 64.10 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 53.92 39.08 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual -86.00 -123.78 37.78 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 6781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1262 0.040 - 0.081: 318 0.081 - 0.121: 163 0.121 - 0.161: 22 0.161 - 0.201: 4 Chirality restraints: 1769 Sorted by residual: chirality pdb=" CA ILE L 31 " pdb=" N ILE L 31 " pdb=" C ILE L 31 " pdb=" CB ILE L 31 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE C 90 " pdb=" N ILE C 90 " pdb=" C ILE C 90 " pdb=" CB ILE C 90 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 1766 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " 0.021 2.00e-02 2.50e+03 1.94e-02 9.38e+00 pdb=" CG TRP D 36 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 346 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 347 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 215 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO C 216 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " 0.026 5.00e-02 4.00e+02 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 342 2.71 - 3.26: 10914 3.26 - 3.81: 17797 3.81 - 4.35: 22488 4.35 - 4.90: 38853 Nonbonded interactions: 90394 Sorted by model distance: nonbonded pdb=" OH TYR B 248 " pdb=" O PRO B 283 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR A 248 " pdb=" O PRO A 283 " model vdw 2.173 3.040 nonbonded pdb=" O VAL A 213 " pdb=" OG1 THR A 227 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN B 84 " pdb=" OH TYR B 274 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR C 248 " pdb=" O PRO C 283 " model vdw 2.255 3.040 ... (remaining 90389 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } 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: 8.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.750 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11257 Z= 0.178 Angle : 0.638 11.559 15285 Z= 0.373 Chirality : 0.046 0.201 1769 Planarity : 0.004 0.048 1934 Dihedral : 14.821 88.412 4091 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.32 % Allowed : 15.20 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.37 (0.22), residues: 1405 helix: 0.25 (0.30), residues: 300 sheet: -0.18 (0.26), residues: 416 loop : -0.38 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 375 TYR 0.028 0.001 TYR A 79 PHE 0.027 0.001 PHE H 29 TRP 0.050 0.002 TRP D 36 HIS 0.004 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00309 (11238) covalent geometry : angle 0.63806 (15247) SS BOND : bond 0.00194 ( 19) SS BOND : angle 0.67122 ( 38) hydrogen bonds : bond 0.22555 ( 477) hydrogen bonds : angle 8.70543 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 0.373 Fit side-chains REVERT: A 268 TYR cc_start: 0.7947 (t80) cc_final: 0.7625 (t80) REVERT: A 350 ASN cc_start: 0.7518 (t0) cc_final: 0.7291 (t0) outliers start: 4 outliers final: 3 residues processed: 204 average time/residue: 0.1018 time to fit residues: 29.8852 Evaluate side-chains 201 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 316 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 64 ASN A 217 ASN A 219 GLN A 303 ASN A 320 ASN A 325 ASN B 217 ASN B 289 GLN B 414 ASN C 194 GLN C 325 ASN C 393 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124417 restraints weight = 14825.150| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.90 r_work: 0.3520 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11257 Z= 0.240 Angle : 0.635 6.368 15285 Z= 0.333 Chirality : 0.048 0.184 1769 Planarity : 0.005 0.046 1934 Dihedral : 5.885 57.939 1537 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.04 % Allowed : 13.76 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.62 (0.22), residues: 1405 helix: 0.16 (0.28), residues: 315 sheet: -0.38 (0.26), residues: 399 loop : -0.58 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.027 0.002 TYR E 49 PHE 0.016 0.002 PHE C 282 TRP 0.027 0.002 TRP D 36 HIS 0.006 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00557 (11238) covalent geometry : angle 0.63435 (15247) SS BOND : bond 0.00332 ( 19) SS BOND : angle 0.86173 ( 38) hydrogen bonds : bond 0.04478 ( 477) hydrogen bonds : angle 5.66534 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.7861 (tp40) cc_final: 0.7592 (tp-100) REVERT: B 220 ASP cc_start: 0.6568 (t0) cc_final: 0.6368 (t0) REVERT: B 223 SER cc_start: 0.7934 (t) cc_final: 0.7723 (m) REVERT: B 271 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7752 (mp) REVERT: B 273 SER cc_start: 0.8311 (t) cc_final: 0.7940 (p) REVERT: B 365 ARG cc_start: 0.6713 (ptp90) cc_final: 0.6267 (ptp90) REVERT: C 30 TYR cc_start: 0.7993 (m-80) cc_final: 0.7591 (m-80) REVERT: D 36 TRP cc_start: 0.7153 (m100) cc_final: 0.6874 (m100) outliers start: 38 outliers final: 23 residues processed: 246 average time/residue: 0.1015 time to fit residues: 36.0518 Evaluate side-chains 240 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 110 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 424 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125807 restraints weight = 14962.695| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.91 r_work: 0.3525 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11257 Z= 0.197 Angle : 0.597 7.910 15285 Z= 0.309 Chirality : 0.047 0.183 1769 Planarity : 0.004 0.045 1934 Dihedral : 5.281 43.937 1531 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.68 % Allowed : 14.80 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.62 (0.22), residues: 1405 helix: 0.32 (0.29), residues: 315 sheet: -0.37 (0.26), residues: 401 loop : -0.68 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.024 0.001 TYR E 49 PHE 0.017 0.001 PHE C 282 TRP 0.015 0.002 TRP B 308 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00459 (11238) covalent geometry : angle 0.59607 (15247) SS BOND : bond 0.00411 ( 19) SS BOND : angle 0.77248 ( 38) hydrogen bonds : bond 0.03948 ( 477) hydrogen bonds : angle 5.28502 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6253 (OUTLIER) cc_final: 0.5871 (mt) REVERT: A 38 LEU cc_start: 0.8394 (mt) cc_final: 0.8082 (mp) REVERT: A 294 GLN cc_start: 0.7841 (tp40) cc_final: 0.7597 (tp40) REVERT: B 271 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7748 (mp) REVERT: B 273 SER cc_start: 0.8257 (t) cc_final: 0.7928 (p) REVERT: B 365 ARG cc_start: 0.6699 (ptp90) cc_final: 0.6199 (ptp90) REVERT: B 425 VAL cc_start: 0.8234 (t) cc_final: 0.7866 (p) REVERT: C 30 TYR cc_start: 0.7958 (m-80) cc_final: 0.7568 (m-80) REVERT: E 91 PHE cc_start: 0.7851 (p90) cc_final: 0.7481 (p90) outliers start: 46 outliers final: 29 residues processed: 232 average time/residue: 0.0940 time to fit residues: 32.1647 Evaluate side-chains 230 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 303 ASN A 325 ASN B 224 ASN B 414 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124088 restraints weight = 14889.658| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.90 r_work: 0.3513 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11257 Z= 0.258 Angle : 0.631 7.604 15285 Z= 0.327 Chirality : 0.049 0.189 1769 Planarity : 0.004 0.046 1934 Dihedral : 5.578 57.156 1531 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.16 % Allowed : 15.76 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.78 (0.22), residues: 1405 helix: 0.22 (0.29), residues: 318 sheet: -0.50 (0.25), residues: 413 loop : -0.79 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.030 0.002 TYR E 49 PHE 0.015 0.002 PHE L 91 TRP 0.017 0.002 TRP E 92 HIS 0.005 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00606 (11238) covalent geometry : angle 0.63004 (15247) SS BOND : bond 0.00372 ( 19) SS BOND : angle 0.88511 ( 38) hydrogen bonds : bond 0.04039 ( 477) hydrogen bonds : angle 5.28486 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.5901 (mt) REVERT: A 294 GLN cc_start: 0.7830 (tp40) cc_final: 0.7559 (tp40) REVERT: B 271 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7757 (mp) REVERT: B 273 SER cc_start: 0.8299 (t) cc_final: 0.7980 (p) REVERT: B 365 ARG cc_start: 0.6718 (ptp90) cc_final: 0.6195 (ptp90) REVERT: B 396 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7262 (p) REVERT: C 30 TYR cc_start: 0.7976 (m-80) cc_final: 0.7583 (m-80) REVERT: C 316 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (mp) REVERT: D 36 TRP cc_start: 0.7232 (m100) cc_final: 0.6955 (m100) REVERT: E 91 PHE cc_start: 0.7966 (p90) cc_final: 0.7722 (p90) outliers start: 52 outliers final: 34 residues processed: 247 average time/residue: 0.0945 time to fit residues: 34.5597 Evaluate side-chains 254 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 80 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125238 restraints weight = 14834.156| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.91 r_work: 0.3528 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11257 Z= 0.204 Angle : 0.600 9.613 15285 Z= 0.309 Chirality : 0.047 0.191 1769 Planarity : 0.004 0.046 1934 Dihedral : 5.402 56.550 1531 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.24 % Allowed : 16.32 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.75 (0.22), residues: 1405 helix: 0.25 (0.29), residues: 321 sheet: -0.47 (0.25), residues: 413 loop : -0.78 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.028 0.002 TYR A 79 PHE 0.017 0.002 PHE B 282 TRP 0.015 0.002 TRP B 308 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00478 (11238) covalent geometry : angle 0.59902 (15247) SS BOND : bond 0.00308 ( 19) SS BOND : angle 0.92394 ( 38) hydrogen bonds : bond 0.03726 ( 477) hydrogen bonds : angle 5.13699 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5922 (mt) REVERT: B 271 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7718 (mt) REVERT: B 342 GLN cc_start: 0.7065 (pm20) cc_final: 0.6731 (pm20) REVERT: B 365 ARG cc_start: 0.6728 (ptp90) cc_final: 0.6220 (ptp90) REVERT: B 396 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7295 (p) REVERT: B 425 VAL cc_start: 0.8237 (t) cc_final: 0.7850 (p) REVERT: C 30 TYR cc_start: 0.7973 (m-80) cc_final: 0.7668 (m-80) REVERT: C 316 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8080 (mp) REVERT: D 36 TRP cc_start: 0.7186 (m100) cc_final: 0.6832 (m100) REVERT: E 91 PHE cc_start: 0.7982 (p90) cc_final: 0.7747 (p90) outliers start: 53 outliers final: 36 residues processed: 240 average time/residue: 0.0970 time to fit residues: 34.4236 Evaluate side-chains 246 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 18 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.0370 chunk 108 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN ** C 424 ASN ** 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 = 0.3909 r_free = 0.3909 target = 0.148633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127840 restraints weight = 14731.828| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.90 r_work: 0.3558 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11257 Z= 0.129 Angle : 0.550 9.006 15285 Z= 0.283 Chirality : 0.046 0.193 1769 Planarity : 0.004 0.044 1934 Dihedral : 5.046 56.200 1531 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.68 % Allowed : 17.52 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.22), residues: 1405 helix: 0.50 (0.29), residues: 315 sheet: -0.42 (0.25), residues: 407 loop : -0.73 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.027 0.001 TYR A 79 PHE 0.014 0.001 PHE B 282 TRP 0.011 0.001 TRP B 308 HIS 0.003 0.000 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00294 (11238) covalent geometry : angle 0.54903 (15247) SS BOND : bond 0.00394 ( 19) SS BOND : angle 0.72728 ( 38) hydrogen bonds : bond 0.03327 ( 477) hydrogen bonds : angle 4.91175 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5872 (mt) REVERT: A 320 ASN cc_start: 0.7279 (m-40) cc_final: 0.6920 (m110) REVERT: B 271 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7655 (mt) REVERT: B 273 SER cc_start: 0.8257 (t) cc_final: 0.7901 (p) REVERT: B 323 ILE cc_start: 0.8407 (mt) cc_final: 0.8148 (mt) REVERT: B 365 ARG cc_start: 0.6732 (ptp90) cc_final: 0.6195 (ptp90) REVERT: B 396 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7305 (p) REVERT: B 425 VAL cc_start: 0.8214 (t) cc_final: 0.7852 (p) REVERT: C 30 TYR cc_start: 0.7943 (m-80) cc_final: 0.7573 (m-80) REVERT: C 316 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8031 (mp) REVERT: D 36 TRP cc_start: 0.7152 (m100) cc_final: 0.6820 (m100) REVERT: E 91 PHE cc_start: 0.7948 (p90) cc_final: 0.7721 (p90) outliers start: 46 outliers final: 31 residues processed: 234 average time/residue: 0.0974 time to fit residues: 33.5368 Evaluate side-chains 239 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 127 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 139 optimal weight: 0.0010 chunk 75 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN B 325 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.148958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128392 restraints weight = 14708.149| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.89 r_work: 0.3570 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11257 Z= 0.117 Angle : 0.537 9.826 15285 Z= 0.274 Chirality : 0.045 0.174 1769 Planarity : 0.004 0.044 1934 Dihedral : 4.863 56.658 1531 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.20 % Allowed : 17.44 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.45 (0.22), residues: 1405 helix: 0.71 (0.30), residues: 315 sheet: -0.33 (0.25), residues: 407 loop : -0.68 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.026 0.001 TYR A 79 PHE 0.011 0.001 PHE L 91 TRP 0.010 0.001 TRP B 308 HIS 0.003 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00265 (11238) covalent geometry : angle 0.53661 (15247) SS BOND : bond 0.00290 ( 19) SS BOND : angle 0.66750 ( 38) hydrogen bonds : bond 0.03168 ( 477) hydrogen bonds : angle 4.73933 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5900 (mt) REVERT: A 320 ASN cc_start: 0.7283 (m-40) cc_final: 0.6907 (m110) REVERT: B 224 ASN cc_start: 0.7621 (t0) cc_final: 0.7028 (t0) REVERT: B 323 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 365 ARG cc_start: 0.6707 (ptp90) cc_final: 0.6138 (ptp90) REVERT: B 396 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7308 (p) REVERT: B 414 ASN cc_start: 0.7374 (t0) cc_final: 0.7061 (t0) REVERT: B 425 VAL cc_start: 0.8184 (t) cc_final: 0.7830 (p) REVERT: C 30 TYR cc_start: 0.7966 (m-80) cc_final: 0.7678 (m-80) REVERT: D 39 GLN cc_start: 0.7231 (tp40) cc_final: 0.6930 (tp40) REVERT: E 91 PHE cc_start: 0.7928 (p90) cc_final: 0.7723 (p90) outliers start: 40 outliers final: 28 residues processed: 236 average time/residue: 0.0867 time to fit residues: 30.1217 Evaluate side-chains 240 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 0.0010 chunk 71 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 303 ASN B 51 ASN B 217 ASN B 233 GLN B 325 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125571 restraints weight = 14880.430| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.84 r_work: 0.3529 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11257 Z= 0.217 Angle : 0.605 9.306 15285 Z= 0.308 Chirality : 0.048 0.211 1769 Planarity : 0.004 0.046 1934 Dihedral : 4.996 28.661 1529 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.28 % Allowed : 18.32 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.60 (0.22), residues: 1405 helix: 0.46 (0.29), residues: 321 sheet: -0.38 (0.25), residues: 407 loop : -0.74 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 375 TYR 0.025 0.002 TYR E 49 PHE 0.016 0.002 PHE L 91 TRP 0.014 0.002 TRP E 92 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00514 (11238) covalent geometry : angle 0.60413 (15247) SS BOND : bond 0.00356 ( 19) SS BOND : angle 0.86444 ( 38) hydrogen bonds : bond 0.03559 ( 477) hydrogen bonds : angle 4.91163 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.5970 (mt) REVERT: A 38 LEU cc_start: 0.8332 (mt) cc_final: 0.8060 (mp) REVERT: A 232 SER cc_start: 0.7773 (OUTLIER) cc_final: 0.7448 (t) REVERT: A 320 ASN cc_start: 0.7297 (m-40) cc_final: 0.6931 (m110) REVERT: B 273 SER cc_start: 0.8305 (t) cc_final: 0.7964 (p) REVERT: B 365 ARG cc_start: 0.6756 (ptp90) cc_final: 0.6198 (ptp90) REVERT: B 396 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7255 (p) REVERT: B 414 ASN cc_start: 0.7376 (t0) cc_final: 0.7077 (t0) REVERT: B 425 VAL cc_start: 0.8189 (t) cc_final: 0.7801 (p) REVERT: C 30 TYR cc_start: 0.7958 (m-80) cc_final: 0.7653 (m-80) outliers start: 41 outliers final: 30 residues processed: 244 average time/residue: 0.0948 time to fit residues: 34.0852 Evaluate side-chains 249 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 51 ASN B 233 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.146609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125749 restraints weight = 14712.715| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.90 r_work: 0.3515 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11257 Z= 0.231 Angle : 0.630 10.166 15285 Z= 0.320 Chirality : 0.049 0.212 1769 Planarity : 0.004 0.046 1934 Dihedral : 5.150 31.509 1529 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.60 % Allowed : 18.40 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.22), residues: 1405 helix: 0.38 (0.29), residues: 321 sheet: -0.54 (0.25), residues: 415 loop : -0.74 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 375 TYR 0.027 0.002 TYR E 49 PHE 0.023 0.002 PHE E 91 TRP 0.018 0.002 TRP E 92 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00544 (11238) covalent geometry : angle 0.62948 (15247) SS BOND : bond 0.00367 ( 19) SS BOND : angle 0.93294 ( 38) hydrogen bonds : bond 0.03645 ( 477) hydrogen bonds : angle 4.98096 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.5980 (mt) REVERT: A 320 ASN cc_start: 0.7320 (m-40) cc_final: 0.6956 (m110) REVERT: B 28 LEU cc_start: 0.7709 (mt) cc_final: 0.7454 (mt) REVERT: B 224 ASN cc_start: 0.7592 (t0) cc_final: 0.7104 (t0) REVERT: B 365 ARG cc_start: 0.6777 (ptp90) cc_final: 0.6242 (ptp90) REVERT: B 396 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7271 (p) REVERT: B 414 ASN cc_start: 0.7408 (t0) cc_final: 0.7102 (t0) REVERT: C 30 TYR cc_start: 0.7963 (m-80) cc_final: 0.7651 (m-80) REVERT: D 39 GLN cc_start: 0.7326 (tp40) cc_final: 0.7048 (tp40) REVERT: E 91 PHE cc_start: 0.7815 (p90) cc_final: 0.7295 (p90) outliers start: 45 outliers final: 34 residues processed: 249 average time/residue: 0.0943 time to fit residues: 34.7611 Evaluate side-chains 254 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 134 optimal weight: 0.0970 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 233 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127435 restraints weight = 14904.606| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.92 r_work: 0.3536 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11257 Z= 0.156 Angle : 0.586 11.254 15285 Z= 0.296 Chirality : 0.047 0.208 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.927 29.144 1529 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.88 % Allowed : 19.12 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.60 (0.22), residues: 1405 helix: 0.62 (0.30), residues: 315 sheet: -0.40 (0.25), residues: 407 loop : -0.80 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 375 TYR 0.024 0.001 TYR A 79 PHE 0.016 0.001 PHE E 91 TRP 0.015 0.001 TRP E 92 HIS 0.003 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00366 (11238) covalent geometry : angle 0.58504 (15247) SS BOND : bond 0.00298 ( 19) SS BOND : angle 0.80299 ( 38) hydrogen bonds : bond 0.03316 ( 477) hydrogen bonds : angle 4.84450 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.5913 (mt) REVERT: A 38 LEU cc_start: 0.8288 (mt) cc_final: 0.7994 (mp) REVERT: A 320 ASN cc_start: 0.7336 (m-40) cc_final: 0.6945 (m110) REVERT: B 224 ASN cc_start: 0.7562 (t0) cc_final: 0.7162 (t0) REVERT: B 323 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8075 (mt) REVERT: B 365 ARG cc_start: 0.6762 (ptp90) cc_final: 0.6228 (ptp90) REVERT: B 396 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7272 (p) REVERT: B 414 ASN cc_start: 0.7373 (t0) cc_final: 0.7068 (t0) REVERT: C 30 TYR cc_start: 0.7948 (m-80) cc_final: 0.7644 (m-80) REVERT: D 39 GLN cc_start: 0.7324 (tp40) cc_final: 0.7052 (tp40) REVERT: E 91 PHE cc_start: 0.7793 (p90) cc_final: 0.7486 (p90) outliers start: 36 outliers final: 27 residues processed: 238 average time/residue: 0.0953 time to fit residues: 33.5778 Evaluate side-chains 244 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 75 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 122 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127523 restraints weight = 14925.069| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.86 r_work: 0.3545 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11257 Z= 0.167 Angle : 0.601 12.232 15285 Z= 0.302 Chirality : 0.047 0.208 1769 Planarity : 0.004 0.046 1934 Dihedral : 4.937 28.060 1529 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.64 % Allowed : 19.36 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.58 (0.22), residues: 1405 helix: 0.64 (0.30), residues: 315 sheet: -0.50 (0.25), residues: 415 loop : -0.71 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.024 0.001 TYR A 79 PHE 0.014 0.001 PHE E 91 TRP 0.015 0.002 TRP E 92 HIS 0.004 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00394 (11238) covalent geometry : angle 0.60073 (15247) SS BOND : bond 0.00300 ( 19) SS BOND : angle 0.80703 ( 38) hydrogen bonds : bond 0.03335 ( 477) hydrogen bonds : angle 4.85700 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.08 seconds wall clock time: 54 minutes 19.48 seconds (3259.48 seconds total)