Starting phenix.real_space_refine on Sun Dec 29 17:41:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmj_27541/12_2024/8dmj_27541_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmj_27541/12_2024/8dmj_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_27541/12_2024/8dmj_27541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmj_27541/12_2024/8dmj_27541.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmj_27541/12_2024/8dmj_27541_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmj_27541/12_2024/8dmj_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-5532/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: 8.48, per 1000 atoms: 0.77 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: 2.59 Conformation dependent library (CDL) restraints added in 1.5 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: 1.48 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: 3.71 Time building geometry restraints manager: 3.02 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: 0.00 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: 10.150 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.970 Find NCS groups from input model: 0.350 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- 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 11238 Z= 0.202 Angle : 0.638 11.559 15247 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 *********************** 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 : 1.087 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: 0.2393 time to fit residues: 69.8713 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 : 1.181 ------------------------------------------------------------------------------- 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: 0.0470 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: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11238 Z= 0.290 Angle : 0.600 6.659 15247 Z= 0.315 Chirality : 0.047 0.175 1769 Planarity : 0.004 0.044 1934 Dihedral : 5.699 57.092 1537 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.88 % Allowed : 13.52 % Favored : 83.60 % 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: -0.51 (0.22), residues: 1405 helix: 0.35 (0.29), residues: 309 sheet: -0.34 (0.26), residues: 399 loop : -0.56 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 36 HIS 0.004 0.001 HIS H 99 PHE 0.013 0.002 PHE C 282 TYR 0.024 0.001 TYR E 49 ARG 0.004 0.000 ARG C 375 *********************** 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 249 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.7927 (tp40) cc_final: 0.7703 (tp-100) REVERT: B 223 SER cc_start: 0.7898 (t) cc_final: 0.7678 (m) REVERT: B 254 ASP cc_start: 0.6394 (m-30) cc_final: 0.6183 (m-30) REVERT: B 271 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 273 SER cc_start: 0.8335 (t) cc_final: 0.7964 (p) REVERT: B 365 ARG cc_start: 0.6661 (ptp90) cc_final: 0.6193 (ptp90) REVERT: C 30 TYR cc_start: 0.7988 (m-80) cc_final: 0.7574 (m-80) REVERT: D 5 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7769 (tm-30) REVERT: E 91 PHE cc_start: 0.7868 (p90) cc_final: 0.7497 (p90) outliers start: 36 outliers final: 23 residues processed: 234 average time/residue: 0.2377 time to fit residues: 79.4850 Evaluate side-chains 236 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 102 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11238 Z= 0.264 Angle : 0.574 7.384 15247 Z= 0.298 Chirality : 0.047 0.176 1769 Planarity : 0.004 0.044 1934 Dihedral : 5.132 44.786 1531 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.52 % Allowed : 14.88 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.29), residues: 315 sheet: -0.32 (0.26), residues: 401 loop : -0.59 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 308 HIS 0.003 0.001 HIS H 99 PHE 0.014 0.001 PHE C 282 TYR 0.021 0.001 TYR E 49 ARG 0.004 0.000 ARG C 375 *********************** 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 248 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6155 (OUTLIER) cc_final: 0.5785 (mt) REVERT: A 68 MET cc_start: 0.6085 (ppp) cc_final: 0.5864 (ppp) REVERT: A 294 GLN cc_start: 0.7910 (tp40) cc_final: 0.7692 (tp40) REVERT: B 271 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7802 (mp) REVERT: B 365 ARG cc_start: 0.6649 (ptp90) cc_final: 0.6132 (ptp90) REVERT: B 425 VAL cc_start: 0.8257 (t) cc_final: 0.7924 (p) REVERT: C 30 TYR cc_start: 0.7978 (m-80) cc_final: 0.7576 (m-80) REVERT: E 91 PHE cc_start: 0.7939 (p90) cc_final: 0.7559 (p90) outliers start: 44 outliers final: 28 residues processed: 231 average time/residue: 0.2177 time to fit residues: 73.4027 Evaluate side-chains 228 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 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 324 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 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 125 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 0.0370 chunk 121 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11238 Z= 0.304 Angle : 0.582 8.022 15247 Z= 0.301 Chirality : 0.047 0.185 1769 Planarity : 0.004 0.045 1934 Dihedral : 5.064 30.181 1529 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.76 % Allowed : 15.28 % Favored : 80.96 % 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: -0.58 (0.22), residues: 1405 helix: 0.31 (0.29), residues: 321 sheet: -0.34 (0.25), residues: 413 loop : -0.65 (0.23), residues: 671 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 0.012 0.001 PHE L 91 TYR 0.024 0.001 TYR E 49 ARG 0.003 0.000 ARG C 375 *********************** 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 257 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6194 (OUTLIER) cc_final: 0.5831 (mt) REVERT: A 68 MET cc_start: 0.6134 (ppp) cc_final: 0.5849 (ppp) REVERT: A 361 GLU cc_start: 0.7424 (pm20) cc_final: 0.7185 (pm20) REVERT: B 271 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7822 (mp) REVERT: B 365 ARG cc_start: 0.6683 (ptp90) cc_final: 0.6154 (ptp90) REVERT: B 396 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7337 (p) REVERT: B 425 VAL cc_start: 0.8263 (t) cc_final: 0.7938 (p) REVERT: C 30 TYR cc_start: 0.7957 (m-80) cc_final: 0.7560 (m-80) REVERT: C 226 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7591 (mmt) REVERT: E 91 PHE cc_start: 0.7991 (p90) cc_final: 0.7780 (p90) outliers start: 47 outliers final: 31 residues processed: 238 average time/residue: 0.2261 time to fit residues: 79.1575 Evaluate side-chains 241 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 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 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 226 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain H residue 35 ASP 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 76 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 0.0030 chunk 0 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 303 ASN B 51 ASN B 224 ASN B 414 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11238 Z= 0.250 Angle : 0.576 9.418 15247 Z= 0.294 Chirality : 0.047 0.236 1769 Planarity : 0.004 0.044 1934 Dihedral : 4.931 29.182 1529 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.60 % Allowed : 16.32 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.29), residues: 315 sheet: -0.43 (0.25), residues: 421 loop : -0.60 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 308 HIS 0.003 0.001 HIS H 99 PHE 0.013 0.001 PHE L 91 TYR 0.021 0.001 TYR E 49 ARG 0.003 0.000 ARG C 375 *********************** 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 258 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6154 (OUTLIER) cc_final: 0.5799 (mt) REVERT: A 68 MET cc_start: 0.6156 (ppp) cc_final: 0.5885 (ppp) REVERT: A 361 GLU cc_start: 0.7419 (pm20) cc_final: 0.7032 (pm20) REVERT: B 226 MET cc_start: 0.8368 (mmm) cc_final: 0.8111 (tpt) REVERT: B 365 ARG cc_start: 0.6695 (ptp90) cc_final: 0.6175 (ptp90) REVERT: B 396 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7313 (p) REVERT: B 425 VAL cc_start: 0.8249 (t) cc_final: 0.7928 (p) REVERT: C 30 TYR cc_start: 0.7942 (m-80) cc_final: 0.7554 (m-80) REVERT: C 226 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7614 (mmt) REVERT: D 36 TRP cc_start: 0.7296 (m100) cc_final: 0.6932 (m100) outliers start: 45 outliers final: 30 residues processed: 240 average time/residue: 0.2196 time to fit residues: 76.9288 Evaluate side-chains 242 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 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 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 226 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 135 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11238 Z= 0.334 Angle : 0.606 9.088 15247 Z= 0.310 Chirality : 0.048 0.210 1769 Planarity : 0.004 0.047 1934 Dihedral : 5.106 31.116 1529 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.52 % Allowed : 16.96 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.22), residues: 1405 helix: 0.32 (0.29), residues: 321 sheet: -0.52 (0.25), residues: 415 loop : -0.66 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 92 HIS 0.004 0.001 HIS H 99 PHE 0.017 0.002 PHE E 91 TYR 0.028 0.002 TYR A 79 ARG 0.005 0.000 ARG C 375 *********************** 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 257 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.5861 (mt) REVERT: A 320 ASN cc_start: 0.7211 (m-40) cc_final: 0.6877 (m110) REVERT: A 361 GLU cc_start: 0.7426 (pm20) cc_final: 0.7021 (pm20) REVERT: B 40 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7958 (ttpt) REVERT: B 365 ARG cc_start: 0.6722 (ptp90) cc_final: 0.6166 (ptp90) REVERT: B 396 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7321 (p) REVERT: B 425 VAL cc_start: 0.8271 (t) cc_final: 0.7923 (p) REVERT: C 30 TYR cc_start: 0.7959 (m-80) cc_final: 0.7638 (m-80) REVERT: C 226 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7600 (mmt) REVERT: D 36 TRP cc_start: 0.7317 (m100) cc_final: 0.6964 (m100) REVERT: E 91 PHE cc_start: 0.7861 (p90) cc_final: 0.7468 (p90) outliers start: 44 outliers final: 34 residues processed: 241 average time/residue: 0.2197 time to fit residues: 76.8275 Evaluate side-chains 249 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 258 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 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 226 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 35 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.0030 chunk 114 optimal weight: 0.3980 chunk 75 optimal weight: 0.2980 chunk 134 optimal weight: 0.0980 chunk 84 optimal weight: 0.0980 chunk 82 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.1980 overall best weight: 0.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 320 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11238 Z= 0.140 Angle : 0.523 9.090 15247 Z= 0.266 Chirality : 0.045 0.181 1769 Planarity : 0.004 0.046 1934 Dihedral : 4.547 23.604 1529 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.64 % Allowed : 17.52 % Favored : 79.84 % 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: 0.79 (0.30), residues: 315 sheet: -0.34 (0.25), residues: 420 loop : -0.60 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 92 HIS 0.003 0.001 HIS B 29 PHE 0.010 0.001 PHE C 214 TYR 0.028 0.001 TYR A 79 ARG 0.005 0.000 ARG C 375 *********************** 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 251 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 GLU cc_start: 0.7413 (pm20) cc_final: 0.7031 (pm20) REVERT: B 365 ARG cc_start: 0.6729 (ptp90) cc_final: 0.6171 (ptp90) REVERT: B 425 VAL cc_start: 0.8198 (t) cc_final: 0.7914 (p) REVERT: C 30 TYR cc_start: 0.7917 (m-80) cc_final: 0.7540 (m-80) REVERT: D 39 GLN cc_start: 0.7333 (tp40) cc_final: 0.7056 (tp40) REVERT: E 91 PHE cc_start: 0.7710 (p90) cc_final: 0.7349 (p90) outliers start: 33 outliers final: 22 residues processed: 238 average time/residue: 0.2270 time to fit residues: 76.4239 Evaluate side-chains 238 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 366 GLU Chi-restraints excluded: chain B residue 59 ILE 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 68 MET Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 51 ASN B 217 ASN B 424 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11238 Z= 0.413 Angle : 0.644 9.413 15247 Z= 0.327 Chirality : 0.049 0.205 1769 Planarity : 0.004 0.045 1934 Dihedral : 5.129 30.209 1529 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.04 % Allowed : 18.16 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.22), residues: 1405 helix: 0.48 (0.29), residues: 315 sheet: -0.49 (0.25), residues: 415 loop : -0.69 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 92 HIS 0.005 0.001 HIS H 99 PHE 0.018 0.002 PHE L 91 TYR 0.029 0.002 TYR E 49 ARG 0.006 0.000 ARG C 375 *********************** 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 256 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8547 (mt) cc_final: 0.8317 (mp) REVERT: A 361 GLU cc_start: 0.7433 (pm20) cc_final: 0.6992 (pm20) REVERT: B 365 ARG cc_start: 0.6760 (ptp90) cc_final: 0.6226 (ptp90) REVERT: B 396 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7325 (p) REVERT: B 425 VAL cc_start: 0.8263 (t) cc_final: 0.7906 (p) REVERT: C 30 TYR cc_start: 0.7965 (m-80) cc_final: 0.7635 (m-80) REVERT: E 91 PHE cc_start: 0.7976 (p90) cc_final: 0.7573 (p90) outliers start: 38 outliers final: 27 residues processed: 242 average time/residue: 0.2371 time to fit residues: 83.9950 Evaluate side-chains 242 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 312 VAL 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 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 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 55 LYS 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 424 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.3980 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 217 ASN B 424 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11238 Z= 0.291 Angle : 0.602 10.614 15247 Z= 0.304 Chirality : 0.047 0.199 1769 Planarity : 0.004 0.046 1934 Dihedral : 4.998 29.841 1529 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.64 % Allowed : 19.36 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.22), residues: 1405 helix: 0.47 (0.29), residues: 315 sheet: -0.49 (0.25), residues: 415 loop : -0.69 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 92 HIS 0.003 0.001 HIS H 99 PHE 0.015 0.001 PHE L 91 TYR 0.024 0.001 TYR E 49 ARG 0.007 0.000 ARG C 375 *********************** 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 248 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8507 (mt) cc_final: 0.8257 (mp) REVERT: A 361 GLU cc_start: 0.7425 (pm20) cc_final: 0.7005 (pm20) REVERT: B 365 ARG cc_start: 0.6766 (ptp90) cc_final: 0.6235 (ptp90) REVERT: B 396 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7346 (p) REVERT: C 30 TYR cc_start: 0.7943 (m-80) cc_final: 0.7626 (m-80) REVERT: D 39 GLN cc_start: 0.7400 (tp40) cc_final: 0.7152 (tp40) REVERT: E 91 PHE cc_start: 0.7936 (p90) cc_final: 0.7561 (p90) outliers start: 33 outliers final: 25 residues processed: 237 average time/residue: 0.2201 time to fit residues: 75.8766 Evaluate side-chains 241 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 312 VAL 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 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 55 LYS Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain L residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 139 optimal weight: 0.3980 chunk 128 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11238 Z= 0.364 Angle : 0.647 13.737 15247 Z= 0.326 Chirality : 0.049 0.224 1769 Planarity : 0.005 0.050 1934 Dihedral : 5.192 31.755 1529 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.48 % Allowed : 19.28 % Favored : 78.24 % 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: -0.75 (0.22), residues: 1405 helix: 0.41 (0.29), residues: 315 sheet: -0.57 (0.25), residues: 415 loop : -0.79 (0.23), residues: 675 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 0.016 0.002 PHE L 91 TYR 0.029 0.002 TYR E 49 ARG 0.008 0.000 ARG C 375 ********************** 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 252 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8512 (mt) cc_final: 0.8284 (mp) REVERT: A 294 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7603 (tp-100) REVERT: A 361 GLU cc_start: 0.7429 (pm20) cc_final: 0.7023 (pm20) REVERT: B 365 ARG cc_start: 0.6768 (ptp90) cc_final: 0.6244 (ptp90) REVERT: B 396 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7329 (p) REVERT: B 425 VAL cc_start: 0.8256 (t) cc_final: 0.7884 (p) REVERT: C 30 TYR cc_start: 0.7949 (m-80) cc_final: 0.7629 (m-80) REVERT: E 91 PHE cc_start: 0.7985 (p90) cc_final: 0.7574 (p90) REVERT: L 4 MET cc_start: 0.7875 (mmm) cc_final: 0.6945 (mmm) outliers start: 31 outliers final: 26 residues processed: 240 average time/residue: 0.2179 time to fit residues: 75.9975 Evaluate side-chains 246 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 312 VAL 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 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 363 CYS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 55 LYS 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 424 ASN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain L residue 19 VAL 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 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 233 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.146091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125300 restraints weight = 14798.873| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.91 r_work: 0.3525 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11238 Z= 0.320 Angle : 0.624 11.772 15247 Z= 0.314 Chirality : 0.048 0.214 1769 Planarity : 0.004 0.045 1934 Dihedral : 5.105 31.179 1529 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.32 % Allowed : 19.36 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.22), residues: 1405 helix: 0.46 (0.29), residues: 315 sheet: -0.57 (0.25), residues: 415 loop : -0.80 (0.23), residues: 675 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 0.015 0.002 PHE L 91 TYR 0.026 0.002 TYR E 49 ARG 0.009 0.000 ARG C 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.11 seconds wall clock time: 56 minutes 5.92 seconds (3365.92 seconds total)