Starting phenix.real_space_refine on Tue Jul 29 05:36:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmj_27541/07_2025/8dmj_27541_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmj_27541/07_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_27541/07_2025/8dmj_27541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmj_27541/07_2025/8dmj_27541.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmj_27541/07_2025/8dmj_27541_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmj_27541/07_2025/8dmj_27541_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.39, per 1000 atoms: 0.76 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: 2.80 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.41 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: 3.70 Time building geometry restraints manager: 3.42 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: 465.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.760 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 500.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (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 TRP 0.050 0.002 TRP D 36 HIS 0.004 0.001 HIS E 30 PHE 0.027 0.001 PHE H 29 TYR 0.028 0.001 TYR A 79 ARG 0.006 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.22555 ( 477) hydrogen bonds : angle 8.70543 ( 1266) SS BOND : bond 0.00194 ( 19) SS BOND : angle 0.67122 ( 38) covalent geometry : bond 0.00309 (11238) covalent geometry : angle 0.63806 (15247) *********************** 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 : 1.248 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: 0.2352 time to fit residues: 68.8003 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 : 1.058 ------------------------------------------------------------------------------- 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 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.147507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126494 restraints weight = 14784.573| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.89 r_work: 0.3530 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11257 Z= 0.201 Angle : 0.606 6.489 15285 Z= 0.318 Chirality : 0.047 0.177 1769 Planarity : 0.004 0.044 1934 Dihedral : 5.752 57.039 1537 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.88 % Allowed : 13.68 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1405 helix: 0.33 (0.29), residues: 309 sheet: -0.34 (0.26), residues: 399 loop : -0.57 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 36 HIS 0.005 0.001 HIS H 99 PHE 0.014 0.002 PHE C 282 TYR 0.024 0.002 TYR E 49 ARG 0.004 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 477) hydrogen bonds : angle 5.58429 ( 1266) SS BOND : bond 0.00300 ( 19) SS BOND : angle 0.81994 ( 38) covalent geometry : bond 0.00463 (11238) covalent geometry : angle 0.60519 (15247) *********************** 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 258 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.7845 (tp40) cc_final: 0.7619 (tp-100) REVERT: B 223 SER cc_start: 0.7934 (t) cc_final: 0.7721 (m) REVERT: B 254 ASP cc_start: 0.6399 (m-30) cc_final: 0.6182 (m-30) REVERT: B 271 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7725 (mp) REVERT: B 273 SER cc_start: 0.8277 (t) cc_final: 0.7926 (p) REVERT: B 365 ARG cc_start: 0.6713 (ptp90) cc_final: 0.6238 (ptp90) REVERT: C 30 TYR cc_start: 0.7978 (m-80) cc_final: 0.7571 (m-80) REVERT: C 246 LEU cc_start: 0.8485 (mt) cc_final: 0.8262 (mt) REVERT: D 36 TRP cc_start: 0.7121 (m100) cc_final: 0.6853 (m100) REVERT: E 91 PHE cc_start: 0.7826 (p90) cc_final: 0.7432 (p90) outliers start: 36 outliers final: 23 residues processed: 243 average time/residue: 0.2309 time to fit residues: 80.5748 Evaluate side-chains 244 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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 335 LYS 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 122 optimal weight: 0.2980 chunk 94 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 135 optimal weight: 0.0030 chunk 114 optimal weight: 0.8980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127629 restraints weight = 14859.598| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.91 r_work: 0.3549 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11257 Z= 0.141 Angle : 0.551 7.674 15285 Z= 0.287 Chirality : 0.046 0.169 1769 Planarity : 0.004 0.042 1934 Dihedral : 5.009 44.690 1531 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.96 % Allowed : 15.36 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1405 helix: 0.46 (0.29), residues: 315 sheet: -0.29 (0.26), residues: 401 loop : -0.56 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 308 HIS 0.003 0.001 HIS E 30 PHE 0.011 0.001 PHE L 91 TYR 0.018 0.001 TYR E 49 ARG 0.003 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 477) hydrogen bonds : angle 5.18052 ( 1266) SS BOND : bond 0.00300 ( 19) SS BOND : angle 0.68806 ( 38) covalent geometry : bond 0.00321 (11238) covalent geometry : angle 0.55097 (15247) *********************** 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 246 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 271 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7710 (mp) REVERT: B 365 ARG cc_start: 0.6671 (ptp90) cc_final: 0.6157 (ptp90) REVERT: B 425 VAL cc_start: 0.8221 (t) cc_final: 0.7872 (p) REVERT: C 30 TYR cc_start: 0.7966 (m-80) cc_final: 0.7581 (m-80) REVERT: D 36 TRP cc_start: 0.7184 (m100) cc_final: 0.6918 (m100) REVERT: E 91 PHE cc_start: 0.7870 (p90) cc_final: 0.7555 (p90) outliers start: 37 outliers final: 24 residues processed: 233 average time/residue: 0.2203 time to fit residues: 72.9661 Evaluate side-chains 229 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 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 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 H residue 35 ASP 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 51 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 126 optimal weight: 0.0670 chunk 121 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 325 ASN B 51 ASN B 224 ASN B 325 ASN B 414 ASN B 424 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 = 0.3893 r_free = 0.3893 target = 0.147025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126113 restraints weight = 14683.981| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.89 r_work: 0.3529 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11257 Z= 0.194 Angle : 0.580 8.116 15285 Z= 0.299 Chirality : 0.047 0.181 1769 Planarity : 0.004 0.045 1934 Dihedral : 5.017 29.295 1529 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.52 % Allowed : 15.68 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1405 helix: 0.39 (0.29), residues: 321 sheet: -0.34 (0.26), residues: 401 loop : -0.60 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 308 HIS 0.004 0.001 HIS H 99 PHE 0.013 0.001 PHE C 282 TYR 0.023 0.001 TYR E 49 ARG 0.004 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 477) hydrogen bonds : angle 5.08251 ( 1266) SS BOND : bond 0.00325 ( 19) SS BOND : angle 0.77913 ( 38) covalent geometry : bond 0.00454 (11238) covalent geometry : angle 0.57892 (15247) *********************** 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 255 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6240 (OUTLIER) cc_final: 0.5844 (mt) REVERT: A 361 GLU cc_start: 0.7440 (pm20) cc_final: 0.7207 (pm20) REVERT: B 271 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7777 (mp) REVERT: B 365 ARG cc_start: 0.6708 (ptp90) cc_final: 0.6153 (ptp90) REVERT: B 396 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7289 (p) REVERT: B 425 VAL cc_start: 0.8204 (t) cc_final: 0.7855 (p) REVERT: C 30 TYR cc_start: 0.7953 (m-80) cc_final: 0.7558 (m-80) REVERT: E 91 PHE cc_start: 0.7958 (p90) cc_final: 0.7709 (p90) outliers start: 44 outliers final: 30 residues processed: 237 average time/residue: 0.2055 time to fit residues: 71.2895 Evaluate side-chains 241 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 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 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 335 LYS Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 110 THR 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 13 optimal weight: 0.4980 chunk 14 optimal weight: 0.0870 chunk 137 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 124 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 0.2358 ------------------------------------------------------------------------------- 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 224 ASN B 424 ASN ** 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 = 0.3915 r_free = 0.3915 target = 0.148920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128274 restraints weight = 14803.775| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.90 r_work: 0.3555 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11257 Z= 0.121 Angle : 0.536 8.834 15285 Z= 0.276 Chirality : 0.045 0.168 1769 Planarity : 0.004 0.042 1934 Dihedral : 4.720 26.121 1529 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.44 % Allowed : 16.40 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1405 helix: 0.67 (0.29), residues: 315 sheet: -0.27 (0.25), residues: 413 loop : -0.58 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 308 HIS 0.003 0.000 HIS E 30 PHE 0.013 0.001 PHE B 282 TYR 0.028 0.001 TYR A 79 ARG 0.005 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 477) hydrogen bonds : angle 4.84566 ( 1266) SS BOND : bond 0.00263 ( 19) SS BOND : angle 0.81834 ( 38) covalent geometry : bond 0.00275 (11238) covalent geometry : angle 0.53506 (15247) *********************** 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 242 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5796 (mt) REVERT: A 361 GLU cc_start: 0.7408 (pm20) cc_final: 0.7077 (pm20) REVERT: B 271 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 365 ARG cc_start: 0.6698 (ptp90) cc_final: 0.6139 (ptp90) REVERT: B 396 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7312 (p) REVERT: B 425 VAL cc_start: 0.8179 (t) cc_final: 0.7837 (p) REVERT: C 30 TYR cc_start: 0.7946 (m-80) cc_final: 0.7576 (m-80) REVERT: C 352 MET cc_start: 0.7481 (mmm) cc_final: 0.6798 (tpt) REVERT: E 91 PHE cc_start: 0.7931 (p90) cc_final: 0.7717 (p90) REVERT: H 82 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5683 (mp) outliers start: 43 outliers final: 29 residues processed: 229 average time/residue: 0.2116 time to fit residues: 71.1010 Evaluate side-chains 227 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 346 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 271 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 4 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 129 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 414 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 = 0.3891 r_free = 0.3891 target = 0.146926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126029 restraints weight = 14915.579| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.90 r_work: 0.3534 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11257 Z= 0.194 Angle : 0.581 8.741 15285 Z= 0.298 Chirality : 0.047 0.193 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.936 28.464 1529 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.92 % Allowed : 16.08 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1405 helix: 0.50 (0.29), residues: 321 sheet: -0.44 (0.25), residues: 421 loop : -0.56 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 308 HIS 0.004 0.001 HIS H 99 PHE 0.014 0.001 PHE L 91 TYR 0.025 0.002 TYR A 79 ARG 0.005 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 477) hydrogen bonds : angle 4.90778 ( 1266) SS BOND : bond 0.00349 ( 19) SS BOND : angle 0.78698 ( 38) covalent geometry : bond 0.00455 (11238) covalent geometry : angle 0.57994 (15247) *********************** 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 250 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5869 (mt) REVERT: A 320 ASN cc_start: 0.7269 (m-40) cc_final: 0.6936 (m110) REVERT: A 361 GLU cc_start: 0.7403 (pm20) cc_final: 0.7010 (pm20) REVERT: B 365 ARG cc_start: 0.6714 (ptp90) cc_final: 0.6185 (ptp90) REVERT: B 396 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7304 (p) REVERT: B 414 ASN cc_start: 0.7390 (OUTLIER) cc_final: 0.7072 (t160) REVERT: B 425 VAL cc_start: 0.8206 (t) cc_final: 0.7853 (p) REVERT: C 30 TYR cc_start: 0.7946 (m-80) cc_final: 0.7631 (m-80) outliers start: 49 outliers final: 36 residues processed: 232 average time/residue: 0.2043 time to fit residues: 69.3734 Evaluate side-chains 241 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 265 GLN 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 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 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 421 VAL 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 110 THR 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 49 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 113 optimal weight: 0.0170 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 414 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 = 0.3901 r_free = 0.3901 target = 0.147804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126840 restraints weight = 14960.192| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.92 r_work: 0.3527 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11257 Z= 0.170 Angle : 0.569 9.437 15285 Z= 0.291 Chirality : 0.046 0.191 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.861 28.294 1529 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.52 % Allowed : 16.24 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1405 helix: 0.46 (0.29), residues: 321 sheet: -0.46 (0.25), residues: 415 loop : -0.55 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 92 HIS 0.003 0.001 HIS E 30 PHE 0.020 0.001 PHE E 91 TYR 0.026 0.001 TYR A 79 ARG 0.004 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 477) hydrogen bonds : angle 4.86403 ( 1266) SS BOND : bond 0.00333 ( 19) SS BOND : angle 0.78962 ( 38) covalent geometry : bond 0.00399 (11238) covalent geometry : angle 0.56817 (15247) *********************** 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 248 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5860 (mt) REVERT: A 320 ASN cc_start: 0.7283 (m-40) cc_final: 0.6939 (m110) REVERT: A 361 GLU cc_start: 0.7433 (pm20) cc_final: 0.7014 (pm20) REVERT: B 365 ARG cc_start: 0.6743 (ptp90) cc_final: 0.6225 (ptp90) REVERT: B 396 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7312 (p) REVERT: B 425 VAL cc_start: 0.8188 (t) cc_final: 0.7831 (p) REVERT: C 30 TYR cc_start: 0.7919 (m-80) cc_final: 0.7614 (m-80) REVERT: C 352 MET cc_start: 0.7266 (mmm) cc_final: 0.7055 (ttm) REVERT: D 39 GLN cc_start: 0.7333 (tp40) cc_final: 0.7006 (tp40) REVERT: E 91 PHE cc_start: 0.7776 (p90) cc_final: 0.7329 (p90) outliers start: 44 outliers final: 35 residues processed: 232 average time/residue: 0.2171 time to fit residues: 74.0287 Evaluate side-chains 238 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 357 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL 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 421 VAL 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 E residue 23 CYS Chi-restraints excluded: chain H residue 110 THR 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 126 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3891 r_free = 0.3891 target = 0.146715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125840 restraints weight = 14857.979| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.90 r_work: 0.3541 rms_B_bonded: 2.03 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: 0.7351 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11257 Z= 0.196 Angle : 0.593 9.589 15285 Z= 0.301 Chirality : 0.047 0.192 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.956 29.377 1529 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.60 % Allowed : 16.80 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1405 helix: 0.39 (0.29), residues: 321 sheet: -0.49 (0.25), residues: 415 loop : -0.60 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 92 HIS 0.004 0.001 HIS H 99 PHE 0.014 0.002 PHE L 91 TYR 0.023 0.002 TYR A 79 ARG 0.004 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 477) hydrogen bonds : angle 4.92376 ( 1266) SS BOND : bond 0.00339 ( 19) SS BOND : angle 0.84862 ( 38) covalent geometry : bond 0.00462 (11238) covalent geometry : angle 0.59174 (15247) *********************** 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 257 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.5921 (mt) REVERT: A 38 LEU cc_start: 0.8314 (mt) cc_final: 0.8030 (mp) REVERT: A 320 ASN cc_start: 0.7277 (m-40) cc_final: 0.6928 (m110) REVERT: A 361 GLU cc_start: 0.7409 (pm20) cc_final: 0.6997 (pm20) REVERT: B 365 ARG cc_start: 0.6748 (ptp90) cc_final: 0.6219 (ptp90) REVERT: B 396 THR cc_start: 0.7537 (OUTLIER) cc_final: 0.7262 (p) REVERT: B 425 VAL cc_start: 0.8203 (t) cc_final: 0.7843 (p) REVERT: E 91 PHE cc_start: 0.7832 (p90) cc_final: 0.7532 (p90) outliers start: 45 outliers final: 36 residues processed: 239 average time/residue: 0.2142 time to fit residues: 75.1137 Evaluate side-chains 249 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 43 THR 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 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 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 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 321 THR Chi-restraints excluded: chain C residue 367 LEU 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 E residue 23 CYS Chi-restraints excluded: chain H residue 110 THR 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 106 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 57 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.126917 restraints weight = 14903.595| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.89 r_work: 0.3551 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11257 Z= 0.154 Angle : 0.568 10.560 15285 Z= 0.287 Chirality : 0.046 0.194 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.807 27.678 1529 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.96 % Allowed : 17.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1405 helix: 0.49 (0.29), residues: 321 sheet: -0.45 (0.26), residues: 415 loop : -0.57 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 92 HIS 0.003 0.001 HIS E 30 PHE 0.012 0.001 PHE L 91 TYR 0.024 0.001 TYR A 79 ARG 0.005 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 477) hydrogen bonds : angle 4.83063 ( 1266) SS BOND : bond 0.00321 ( 19) SS BOND : angle 0.78686 ( 38) covalent geometry : bond 0.00361 (11238) covalent geometry : angle 0.56708 (15247) *********************** 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 246 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6265 (OUTLIER) cc_final: 0.5887 (mt) REVERT: A 320 ASN cc_start: 0.7276 (m-40) cc_final: 0.6918 (m110) REVERT: A 361 GLU cc_start: 0.7405 (pm20) cc_final: 0.6995 (pm20) REVERT: B 365 ARG cc_start: 0.6767 (ptp90) cc_final: 0.6241 (ptp90) REVERT: B 396 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7281 (p) REVERT: B 425 VAL cc_start: 0.8199 (t) cc_final: 0.7836 (p) REVERT: D 39 GLN cc_start: 0.7288 (tp40) cc_final: 0.7013 (tp40) REVERT: E 91 PHE cc_start: 0.7798 (p90) cc_final: 0.7241 (p90) outliers start: 37 outliers final: 32 residues processed: 230 average time/residue: 0.2090 time to fit residues: 69.8358 Evaluate side-chains 244 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 357 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 316 ILE 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 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 367 LEU 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 110 THR 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 3 optimal weight: 0.0070 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.149150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128568 restraints weight = 14820.725| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.89 r_work: 0.3572 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11257 Z= 0.123 Angle : 0.557 11.052 15285 Z= 0.280 Chirality : 0.045 0.175 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.659 24.700 1529 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.72 % Allowed : 18.08 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1405 helix: 0.68 (0.29), residues: 315 sheet: -0.37 (0.26), residues: 415 loop : -0.58 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 92 HIS 0.003 0.000 HIS E 30 PHE 0.011 0.001 PHE L 91 TYR 0.025 0.001 TYR A 79 ARG 0.006 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 477) hydrogen bonds : angle 4.74348 ( 1266) SS BOND : bond 0.00282 ( 19) SS BOND : angle 0.73291 ( 38) covalent geometry : bond 0.00284 (11238) covalent geometry : angle 0.55669 (15247) ********************** 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 241 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6209 (OUTLIER) cc_final: 0.5846 (mt) REVERT: A 320 ASN cc_start: 0.7261 (m-40) cc_final: 0.6894 (m110) REVERT: A 361 GLU cc_start: 0.7400 (pm20) cc_final: 0.7024 (pm20) REVERT: B 72 THR cc_start: 0.8255 (t) cc_final: 0.7895 (t) REVERT: B 365 ARG cc_start: 0.6752 (ptp90) cc_final: 0.6194 (ptp90) REVERT: B 396 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7291 (p) REVERT: B 425 VAL cc_start: 0.8187 (t) cc_final: 0.7860 (p) REVERT: D 39 GLN cc_start: 0.7274 (tp40) cc_final: 0.7000 (tp40) REVERT: E 91 PHE cc_start: 0.7791 (p90) cc_final: 0.7225 (p90) outliers start: 34 outliers final: 29 residues processed: 227 average time/residue: 0.2143 time to fit residues: 70.4415 Evaluate side-chains 237 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 346 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 316 ILE 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 316 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain H residue 110 THR 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 86 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125340 restraints weight = 14765.838| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.88 r_work: 0.3531 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11257 Z= 0.234 Angle : 0.631 11.256 15285 Z= 0.319 Chirality : 0.048 0.203 1769 Planarity : 0.004 0.045 1934 Dihedral : 5.063 29.591 1529 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.04 % Allowed : 17.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1405 helix: 0.36 (0.29), residues: 321 sheet: -0.48 (0.26), residues: 415 loop : -0.66 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 92 HIS 0.004 0.001 HIS H 99 PHE 0.015 0.002 PHE L 91 TYR 0.025 0.002 TYR E 49 ARG 0.009 0.001 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 477) hydrogen bonds : angle 4.92494 ( 1266) SS BOND : bond 0.00372 ( 19) SS BOND : angle 0.95577 ( 38) covalent geometry : bond 0.00554 (11238) covalent geometry : angle 0.62963 (15247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7169.70 seconds wall clock time: 124 minutes 38.93 seconds (7478.93 seconds total)