Starting phenix.real_space_refine on Sat Aug 23 09:03:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmj_27541/08_2025/8dmj_27541_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmj_27541/08_2025/8dmj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmj_27541/08_2025/8dmj_27541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmj_27541/08_2025/8dmj_27541.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmj_27541/08_2025/8dmj_27541_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmj_27541/08_2025/8dmj_27541_neut.cif" } 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-2.0-5787/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: 2.97, per 1000 atoms: 0.27 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: 1.20 Conformation dependent library (CDL) restraints added in 457.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.49 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: 1.99 Time building geometry restraints manager: 1.54 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: 7.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.470 ------------------------------------------------------------------------------- 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 aren 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 : 0.453 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: 0.1026 time to fit residues: 30.2985 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 : 0.421 ------------------------------------------------------------------------------- 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 aren 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 : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.7861 (tp40) cc_final: 0.7591 (tp-100) 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: 0.7753 (mp) REVERT: B 273 SER cc_start: 0.8312 (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: 0.1053 time to fit residues: 37.2684 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 : 0.393 ------------------------------------------------------------------------------- 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 = 0.146794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125869 restraints weight = 14974.743| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.91 r_work: 0.3527 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 0.034 11257 Z= 0.197 Angle : 0.597 7.910 15285 Z= 0.310 Chirality : 0.047 0.183 1769 Planarity : 0.004 0.045 1934 Dihedral : 5.282 43.962 1531 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.68 % Allowed : 14.72 % Favored : 81.60 % 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 aren 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 0.59686 (15247) SS BOND : bond 0.00403 ( 19) SS BOND : angle 0.80337 ( 38) hydrogen bonds : bond 0.03949 ( 477) hydrogen bonds : angle 5.28803 ( 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 252 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5859 (mt) REVERT: A 38 LEU cc_start: 0.8395 (mt) cc_final: 0.8082 (mp) REVERT: A 68 MET cc_start: 0.6146 (ppp) cc_final: 0.5943 (ppp) REVERT: A 294 GLN cc_start: 0.7842 (tp40) cc_final: 0.7596 (tp40) REVERT: B 271 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7733 (mp) REVERT: B 273 SER cc_start: 0.8260 (t) cc_final: 0.7939 (p) REVERT: B 365 ARG cc_start: 0.6710 (ptp90) cc_final: 0.6213 (ptp90) REVERT: B 425 VAL cc_start: 0.8236 (t) cc_final: 0.7873 (p) REVERT: C 30 TYR cc_start: 0.7969 (m-80) cc_final: 0.7580 (m-80) REVERT: E 91 PHE cc_start: 0.7851 (p90) cc_final: 0.7481 (p90) outliers start: 46 outliers final: 29 residues processed: 233 average time/residue: 0.0997 time to fit residues: 34.1718 Evaluate side-chains 231 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 51 ASN B 224 ASN B 325 ASN B 414 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.146039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125065 restraints weight = 14903.347| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.91 r_work: 0.3523 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11257 Z= 0.225 Angle : 0.603 7.765 15285 Z= 0.313 Chirality : 0.048 0.185 1769 Planarity : 0.004 0.046 1934 Dihedral : 5.414 55.880 1531 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.00 % Allowed : 15.68 % Favored : 80.32 % 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 aren not related in a simple way. whole: -0.72 (0.22), residues: 1405 helix: 0.27 (0.29), residues: 321 sheet: -0.46 (0.25), residues: 413 loop : -0.75 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.026 0.002 TYR E 49 PHE 0.014 0.002 PHE L 91 TRP 0.015 0.002 TRP B 308 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00526 (11238) covalent geometry : angle 0.60280 (15247) SS BOND : bond 0.00337 ( 19) SS BOND : angle 0.81108 ( 38) hydrogen bonds : bond 0.03864 ( 477) hydrogen bonds : angle 5.19238 ( 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 259 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5870 (mt) REVERT: A 68 MET cc_start: 0.6111 (ppp) cc_final: 0.5856 (ppp) REVERT: A 294 GLN cc_start: 0.7810 (tp40) cc_final: 0.7555 (tp40) REVERT: B 271 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7771 (mp) REVERT: B 273 SER cc_start: 0.8304 (t) cc_final: 0.7970 (p) REVERT: B 365 ARG cc_start: 0.6712 (ptp90) cc_final: 0.6198 (ptp90) REVERT: B 396 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7287 (p) REVERT: B 425 VAL cc_start: 0.8210 (t) cc_final: 0.7833 (p) REVERT: C 30 TYR cc_start: 0.7979 (m-80) cc_final: 0.7590 (m-80) REVERT: C 316 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8116 (mp) REVERT: E 91 PHE cc_start: 0.7944 (p90) cc_final: 0.7667 (p90) outliers start: 50 outliers final: 33 residues processed: 239 average time/residue: 0.0975 time to fit residues: 34.3763 Evaluate side-chains 244 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 117 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 136 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ** 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 = 0.3885 r_free = 0.3885 target = 0.146214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125340 restraints weight = 14848.817| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.90 r_work: 0.3507 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11257 Z= 0.203 Angle : 0.597 9.812 15285 Z= 0.308 Chirality : 0.047 0.246 1769 Planarity : 0.004 0.046 1934 Dihedral : 5.354 57.955 1531 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.32 % Allowed : 16.24 % 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 aren not related in a simple way. whole: -0.71 (0.22), residues: 1405 helix: 0.30 (0.29), residues: 321 sheet: -0.47 (0.25), residues: 413 loop : -0.76 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.028 0.001 TYR A 79 PHE 0.018 0.002 PHE B 282 TRP 0.014 0.002 TRP B 308 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00474 (11238) covalent geometry : angle 0.59548 (15247) SS BOND : bond 0.00314 ( 19) SS BOND : angle 0.91958 ( 38) hydrogen bonds : bond 0.03708 ( 477) hydrogen bonds : angle 5.08564 ( 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 265 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.5865 (mt) REVERT: B 271 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7771 (mp) REVERT: B 342 GLN cc_start: 0.7046 (pm20) cc_final: 0.6743 (pm20) REVERT: B 365 ARG cc_start: 0.6724 (ptp90) cc_final: 0.6227 (ptp90) REVERT: B 396 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7298 (p) REVERT: B 425 VAL cc_start: 0.8240 (t) cc_final: 0.7858 (p) REVERT: C 30 TYR cc_start: 0.7971 (m-80) cc_final: 0.7670 (m-80) REVERT: D 36 TRP cc_start: 0.7296 (m100) cc_final: 0.6972 (m100) REVERT: E 91 PHE cc_start: 0.7968 (p90) cc_final: 0.7705 (p90) outliers start: 54 outliers final: 36 residues processed: 242 average time/residue: 0.0964 time to fit residues: 34.5300 Evaluate side-chains 247 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 35 LYS 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 238 ASN Chi-restraints excluded: chain B residue 271 LEU 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 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: 0.6980 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 108 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 71 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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 320 ASN ** 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 = 0.3912 r_free = 0.3912 target = 0.148529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127858 restraints weight = 14769.407| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.89 r_work: 0.3559 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1869 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= 0.126 Angle : 0.546 9.088 15285 Z= 0.281 Chirality : 0.046 0.176 1769 Planarity : 0.004 0.044 1934 Dihedral : 4.795 27.914 1529 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.44 % Allowed : 17.28 % Favored : 79.28 % 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 aren not related in a simple way. whole: -0.53 (0.22), residues: 1405 helix: 0.60 (0.29), residues: 315 sheet: -0.37 (0.25), residues: 413 loop : -0.70 (0.23), residues: 677 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 0.011 0.001 PHE L 91 TRP 0.011 0.001 TRP B 308 HIS 0.003 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00289 (11238) covalent geometry : angle 0.54577 (15247) SS BOND : bond 0.00268 ( 19) SS BOND : angle 0.73835 ( 38) hydrogen bonds : bond 0.03294 ( 477) hydrogen bonds : angle 4.85659 ( 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 241 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6181 (OUTLIER) cc_final: 0.5834 (mt) REVERT: A 320 ASN cc_start: 0.7275 (m-40) cc_final: 0.6917 (m110) REVERT: B 84 ASN cc_start: 0.8241 (m-40) cc_final: 0.7943 (m-40) REVERT: B 271 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7614 (mt) REVERT: B 323 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8088 (mt) REVERT: B 365 ARG cc_start: 0.6725 (ptp90) cc_final: 0.6195 (ptp90) REVERT: B 396 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7295 (p) REVERT: B 425 VAL cc_start: 0.8205 (t) cc_final: 0.7847 (p) REVERT: C 30 TYR cc_start: 0.7953 (m-80) cc_final: 0.7580 (m-80) REVERT: E 91 PHE cc_start: 0.7936 (p90) cc_final: 0.7720 (p90) REVERT: H 82 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5724 (mp) outliers start: 43 outliers final: 31 residues processed: 225 average time/residue: 0.0980 time to fit residues: 32.3700 Evaluate side-chains 231 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 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 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 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 H residue 82 LEU 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: 0.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 217 ASN ** 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 = 0.3875 r_free = 0.3875 target = 0.145254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124468 restraints weight = 14708.608| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.88 r_work: 0.3516 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11257 Z= 0.258 Angle : 0.636 9.381 15285 Z= 0.326 Chirality : 0.049 0.219 1769 Planarity : 0.004 0.046 1934 Dihedral : 5.267 32.608 1529 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.84 % Allowed : 17.04 % Favored : 79.12 % 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 aren not related in a simple way. whole: -0.76 (0.22), residues: 1405 helix: 0.31 (0.29), residues: 321 sheet: -0.49 (0.25), residues: 407 loop : -0.81 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.029 0.002 TYR E 49 PHE 0.017 0.002 PHE B 282 TRP 0.017 0.002 TRP E 92 HIS 0.005 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00608 (11238) covalent geometry : angle 0.63476 (15247) SS BOND : bond 0.00414 ( 19) SS BOND : angle 0.96821 ( 38) hydrogen bonds : bond 0.03856 ( 477) hydrogen bonds : angle 5.09462 ( 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 262 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5955 (mt) REVERT: A 232 SER cc_start: 0.7778 (OUTLIER) cc_final: 0.7426 (t) REVERT: A 320 ASN cc_start: 0.7289 (m-40) cc_final: 0.6940 (m110) REVERT: B 271 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7779 (mp) REVERT: B 324 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8433 (p) REVERT: B 365 ARG cc_start: 0.6767 (ptp90) cc_final: 0.6226 (ptp90) REVERT: B 396 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7270 (p) REVERT: B 414 ASN cc_start: 0.7379 (t0) cc_final: 0.7074 (t0) REVERT: C 30 TYR cc_start: 0.7980 (m-80) cc_final: 0.7672 (m-80) REVERT: D 39 GLN cc_start: 0.7400 (tp40) cc_final: 0.7071 (tp40) outliers start: 48 outliers final: 31 residues processed: 246 average time/residue: 0.0974 time to fit residues: 35.4531 Evaluate side-chains 248 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 232 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 263 THR 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 271 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 0.2980 chunk 138 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 106 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 73 optimal weight: 0.0970 chunk 78 optimal weight: 0.4980 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128321 restraints weight = 14946.778| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.89 r_work: 0.3565 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2045 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= 0.121 Angle : 0.555 9.859 15285 Z= 0.282 Chirality : 0.046 0.179 1769 Planarity : 0.004 0.043 1934 Dihedral : 4.762 27.462 1529 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.12 % Allowed : 18.40 % Favored : 78.48 % 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 aren not related in a simple way. whole: -0.52 (0.22), residues: 1405 helix: 0.66 (0.30), residues: 315 sheet: -0.37 (0.25), residues: 407 loop : -0.73 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.028 0.001 TYR C 206 PHE 0.019 0.001 PHE E 91 TRP 0.014 0.001 TRP E 92 HIS 0.004 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00275 (11238) covalent geometry : angle 0.55426 (15247) SS BOND : bond 0.00275 ( 19) SS BOND : angle 0.72987 ( 38) hydrogen bonds : bond 0.03200 ( 477) hydrogen bonds : angle 4.78037 ( 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 244 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 TYR cc_start: 0.8048 (t80) cc_final: 0.7807 (t80) REVERT: B 271 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7673 (mt) REVERT: B 323 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8016 (mt) REVERT: B 365 ARG cc_start: 0.6768 (ptp90) cc_final: 0.6216 (ptp90) REVERT: B 396 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7307 (p) REVERT: B 414 ASN cc_start: 0.7380 (t0) cc_final: 0.7081 (t0) REVERT: C 30 TYR cc_start: 0.7924 (m-80) cc_final: 0.7618 (m-80) REVERT: D 39 GLN cc_start: 0.7315 (tp40) cc_final: 0.6970 (tp40) REVERT: E 32 TYR cc_start: 0.7698 (m-10) cc_final: 0.7373 (m-10) REVERT: E 91 PHE cc_start: 0.7691 (p90) cc_final: 0.7245 (p90) outliers start: 39 outliers final: 25 residues processed: 230 average time/residue: 0.1005 time to fit residues: 33.6324 Evaluate side-chains 229 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 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 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 110 THR Chi-restraints excluded: chain E residue 4 MET 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: 1.9990 chunk 57 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 303 ASN A 320 ASN B 233 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124619 restraints weight = 14732.818| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.89 r_work: 0.3510 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11257 Z= 0.267 Angle : 0.655 10.265 15285 Z= 0.332 Chirality : 0.050 0.222 1769 Planarity : 0.004 0.046 1934 Dihedral : 5.261 32.020 1529 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.12 % Allowed : 18.72 % Favored : 78.16 % 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 aren not related in a simple way. whole: -0.80 (0.22), residues: 1405 helix: 0.33 (0.29), residues: 321 sheet: -0.62 (0.25), residues: 415 loop : -0.79 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 375 TYR 0.029 0.002 TYR E 49 PHE 0.017 0.002 PHE B 282 TRP 0.020 0.002 TRP E 92 HIS 0.005 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00632 (11238) covalent geometry : angle 0.65412 (15247) SS BOND : bond 0.00409 ( 19) SS BOND : angle 1.00294 ( 38) hydrogen bonds : bond 0.03803 ( 477) hydrogen bonds : angle 5.06128 ( 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 256 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.5987 (mt) REVERT: A 268 TYR cc_start: 0.8150 (t80) cc_final: 0.7917 (t80) REVERT: B 271 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7717 (mt) REVERT: B 324 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8406 (p) REVERT: B 365 ARG cc_start: 0.6766 (ptp90) cc_final: 0.6239 (ptp90) REVERT: B 396 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7279 (p) REVERT: B 414 ASN cc_start: 0.7374 (t0) cc_final: 0.7066 (t0) REVERT: C 30 TYR cc_start: 0.7975 (m-80) cc_final: 0.7662 (m-80) REVERT: E 91 PHE cc_start: 0.7913 (p90) cc_final: 0.7536 (p90) outliers start: 39 outliers final: 28 residues processed: 242 average time/residue: 0.0997 time to fit residues: 35.3501 Evaluate side-chains 244 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 320 ASN 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 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 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 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: 0.6980 chunk 139 optimal weight: 0.9990 chunk 86 optimal weight: 0.0870 chunk 37 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 320 ASN B 224 ASN B 233 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126564 restraints weight = 14904.657| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.90 r_work: 0.3538 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11257 Z= 0.163 Angle : 0.608 12.842 15285 Z= 0.305 Chirality : 0.047 0.197 1769 Planarity : 0.004 0.044 1934 Dihedral : 5.016 29.981 1529 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.80 % Allowed : 19.04 % Favored : 78.16 % 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 aren not related in a simple way. whole: -0.65 (0.22), residues: 1405 helix: 0.56 (0.29), residues: 315 sheet: -0.45 (0.25), residues: 407 loop : -0.80 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 375 TYR 0.025 0.001 TYR A 79 PHE 0.015 0.001 PHE E 91 TRP 0.014 0.002 TRP E 92 HIS 0.003 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00383 (11238) covalent geometry : angle 0.60704 (15247) SS BOND : bond 0.00309 ( 19) SS BOND : angle 0.82027 ( 38) hydrogen bonds : bond 0.03369 ( 477) hydrogen bonds : angle 4.90950 ( 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 246 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.5969 (mt) REVERT: A 268 TYR cc_start: 0.8113 (t80) cc_final: 0.7809 (t80) REVERT: B 271 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (mp) REVERT: B 273 SER cc_start: 0.8282 (t) cc_final: 0.7956 (p) REVERT: B 365 ARG cc_start: 0.6763 (ptp90) cc_final: 0.6198 (ptp90) REVERT: B 396 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7312 (p) REVERT: B 414 ASN cc_start: 0.7384 (t0) cc_final: 0.7079 (t0) REVERT: C 30 TYR cc_start: 0.7953 (m-80) cc_final: 0.7647 (m-80) REVERT: D 39 GLN cc_start: 0.7325 (tp40) cc_final: 0.7066 (tp40) REVERT: E 91 PHE cc_start: 0.7833 (p90) cc_final: 0.7497 (p90) outliers start: 35 outliers final: 29 residues processed: 232 average time/residue: 0.0999 time to fit residues: 34.0690 Evaluate side-chains 242 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 320 ASN 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 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 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 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 22 optimal weight: 0.0040 chunk 41 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 0.0020 chunk 17 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 96 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 114 optimal weight: 0.1980 overall best weight: 0.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 217 ASN B 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.150066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129639 restraints weight = 14983.673| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.89 r_work: 0.3585 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11257 Z= 0.108 Angle : 0.560 11.173 15285 Z= 0.282 Chirality : 0.045 0.179 1769 Planarity : 0.004 0.044 1934 Dihedral : 4.666 24.182 1529 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.32 % Allowed : 19.28 % 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 aren not related in a simple way. whole: -0.45 (0.22), residues: 1405 helix: 0.86 (0.30), residues: 315 sheet: -0.30 (0.26), residues: 410 loop : -0.77 (0.23), residues: 680 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 0.012 0.001 PHE E 91 TRP 0.011 0.001 TRP E 92 HIS 0.003 0.000 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00244 (11238) covalent geometry : angle 0.55983 (15247) SS BOND : bond 0.00260 ( 19) SS BOND : angle 0.69071 ( 38) hydrogen bonds : bond 0.03046 ( 477) hydrogen bonds : angle 4.68591 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3193.25 seconds wall clock time: 55 minutes 39.82 seconds (3339.82 seconds total)