Starting phenix.real_space_refine on Wed Sep 17 11:38:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdl_61395/09_2025/9jdl_61395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdl_61395/09_2025/9jdl_61395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jdl_61395/09_2025/9jdl_61395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdl_61395/09_2025/9jdl_61395.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdl_61395/09_2025/9jdl_61395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdl_61395/09_2025/9jdl_61395_neut.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 64 5.16 5 C 5476 2.51 5 N 1212 2.21 5 O 1384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8136 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4040 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 487} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4040 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 487} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.92, per 1000 atoms: 0.24 Number of scatterers: 8136 At special positions: 0 Unit cell: (102.335, 107.61, 98.115, 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 64 16.00 O 1384 8.00 N 1212 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 394.3 milliseconds Enol-peptide restraints added in 1.4 microseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 80.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.529A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.530A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 152 removed outlier: 4.134A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 4.019A pdb=" N ARG A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 178 " --> pdb=" O THR A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 217 through 237 Processing helix chain 'A' and resid 245 through 267 removed outlier: 3.900A pdb=" N THR A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 287 removed outlier: 3.661A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 287' Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.602A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 356 removed outlier: 3.666A pdb=" N GLU A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 4.555A pdb=" N ALA A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.520A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 448 removed outlier: 3.660A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N MET A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.787A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.670A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 471 " --> pdb=" O CYS A 467 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.578A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.367A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.585A pdb=" N CYS A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.536A pdb=" N VAL A 560 " --> pdb=" O CYS A 556 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 65 through 74 removed outlier: 3.530A pdb=" N TYR B 69 " --> pdb=" O TRP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 90 through 106 Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.529A pdb=" N TRP B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 152 removed outlier: 4.134A pdb=" N TYR B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 4.019A pdb=" N ARG B 177 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 178 " --> pdb=" O THR B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 217 through 237 Processing helix chain 'B' and resid 245 through 267 removed outlier: 3.900A pdb=" N THR B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 281 through 287 removed outlier: 3.661A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 287' Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.602A pdb=" N SER B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 356 removed outlier: 3.666A pdb=" N GLU B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 4.555A pdb=" N ALA B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 383 through 416 removed outlier: 3.520A pdb=" N TRP B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 448 removed outlier: 3.661A pdb=" N ILE B 430 " --> pdb=" O TYR B 426 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N MET B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.787A pdb=" N VAL B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 481 removed outlier: 3.670A pdb=" N LEU B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 471 " --> pdb=" O CYS B 467 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.578A pdb=" N GLY B 491 " --> pdb=" O ASN B 487 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 4.366A pdb=" N LYS B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 526 removed outlier: 3.584A pdb=" N CYS B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 555 Processing helix chain 'B' and resid 555 through 567 removed outlier: 3.535A pdb=" N VAL B 560 " --> pdb=" O CYS B 556 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS B 566 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA2, first strand: chain 'B' and resid 531 through 532 515 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.98 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: 2348 1.35 - 1.47: 2389 1.47 - 1.58: 3576 1.58 - 1.70: 1 1.70 - 1.82: 92 Bond restraints: 8406 Sorted by residual: bond pdb=" N VAL B 203 " pdb=" CA VAL B 203 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.36e+00 bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.05e+00 bond pdb=" N LEU B 204 " pdb=" CA LEU B 204 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.31e-02 5.83e+03 7.46e+00 bond pdb=" N ILE B 196 " pdb=" CA ILE B 196 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 7.10e+00 bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.92e+00 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 10900 1.14 - 2.27: 427 2.27 - 3.41: 121 3.41 - 4.54: 21 4.54 - 5.68: 17 Bond angle restraints: 11486 Sorted by residual: angle pdb=" CA PRO B 502 " pdb=" N PRO B 502 " pdb=" CD PRO B 502 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" CA PRO A 502 " pdb=" N PRO A 502 " pdb=" CD PRO A 502 " ideal model delta sigma weight residual 112.00 106.59 5.41 1.40e+00 5.10e-01 1.49e+01 angle pdb=" CA SER B 205 " pdb=" C SER B 205 " pdb=" O SER B 205 " ideal model delta sigma weight residual 122.03 118.26 3.77 1.17e+00 7.31e-01 1.04e+01 angle pdb=" CA GLU B 200 " pdb=" C GLU B 200 " pdb=" O GLU B 200 " ideal model delta sigma weight residual 120.42 117.36 3.06 1.06e+00 8.90e-01 8.35e+00 angle pdb=" CA GLU A 200 " pdb=" C GLU A 200 " pdb=" O GLU A 200 " ideal model delta sigma weight residual 120.42 117.38 3.04 1.06e+00 8.90e-01 8.21e+00 ... (remaining 11481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4395 17.78 - 35.55: 343 35.55 - 53.33: 62 53.33 - 71.10: 10 71.10 - 88.88: 4 Dihedral angle restraints: 4814 sinusoidal: 1870 harmonic: 2944 Sorted by residual: dihedral pdb=" CA GLU B 354 " pdb=" C GLU B 354 " pdb=" N GLN B 355 " pdb=" CA GLN B 355 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLU A 354 " pdb=" C GLU A 354 " pdb=" N GLN A 355 " pdb=" CA GLN A 355 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP A 287 " pdb=" C ASP A 287 " pdb=" N PRO A 288 " pdb=" CA PRO A 288 " ideal model delta harmonic sigma weight residual -180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 947 0.043 - 0.087: 261 0.087 - 0.130: 62 0.130 - 0.173: 4 0.173 - 0.217: 4 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CA ILE A 196 " pdb=" N ILE A 196 " pdb=" C ILE A 196 " pdb=" CB ILE A 196 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B 196 " pdb=" N ILE B 196 " pdb=" C ILE B 196 " pdb=" CB ILE B 196 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" C20 CLR B 701 " pdb=" C17 CLR B 701 " pdb=" C21 CLR B 701 " pdb=" C22 CLR B 701 " both_signs ideal model delta sigma weight residual False 2.59 2.42 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1275 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 501 " -0.077 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO B 502 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 501 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO A 502 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 287 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO B 288 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " 0.020 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 395 2.73 - 3.27: 9497 3.27 - 3.81: 14532 3.81 - 4.36: 17320 4.36 - 4.90: 28144 Nonbonded interactions: 69888 Sorted by model distance: nonbonded pdb=" O VAL A 59 " pdb=" OG SER A 402 " model vdw 2.186 3.040 nonbonded pdb=" O VAL B 59 " pdb=" OG SER B 402 " model vdw 2.187 3.040 nonbonded pdb=" O GLY B 307 " pdb=" OG1 THR B 310 " model vdw 2.197 3.040 nonbonded pdb=" O GLY A 307 " pdb=" OG1 THR A 310 " model vdw 2.198 3.040 nonbonded pdb=" O LEU A 549 " pdb=" OG SER A 552 " model vdw 2.242 3.040 ... (remaining 69883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.820 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 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 0.092 8408 Z= 0.174 Angle : 0.578 5.678 11490 Z= 0.328 Chirality : 0.042 0.217 1278 Planarity : 0.006 0.113 1388 Dihedral : 13.093 88.879 2948 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.25), residues: 1016 helix: 0.50 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -0.40 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.016 0.001 TYR B 137 PHE 0.015 0.001 PHE A 458 TRP 0.013 0.001 TRP B 65 HIS 0.001 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8406) covalent geometry : angle 0.57758 (11486) SS BOND : bond 0.00360 ( 2) SS BOND : angle 1.49932 ( 4) hydrogen bonds : bond 0.25585 ( 515) hydrogen bonds : angle 7.68395 ( 1521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.6667 (ppp) cc_final: 0.6116 (ppp) REVERT: A 173 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 309 MET cc_start: 0.6782 (mmm) cc_final: 0.5996 (mmm) REVERT: A 483 TYR cc_start: 0.6967 (t80) cc_final: 0.6641 (t80) REVERT: B 104 TYR cc_start: 0.5641 (t80) cc_final: 0.5409 (t80) REVERT: B 172 MET cc_start: 0.6267 (ppp) cc_final: 0.5858 (ppp) REVERT: B 173 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7323 (mm-30) REVERT: B 299 PHE cc_start: 0.8020 (m-80) cc_final: 0.7754 (m-80) REVERT: B 306 LEU cc_start: 0.9160 (mp) cc_final: 0.8926 (mp) REVERT: B 327 MET cc_start: 0.8443 (ppp) cc_final: 0.7943 (ppp) REVERT: B 328 LEU cc_start: 0.8839 (mt) cc_final: 0.8371 (mt) REVERT: B 374 TYR cc_start: 0.7930 (m-80) cc_final: 0.7725 (m-80) REVERT: B 437 SER cc_start: 0.8902 (t) cc_final: 0.8583 (p) REVERT: B 483 TYR cc_start: 0.6771 (t80) cc_final: 0.6053 (t80) REVERT: B 554 MET cc_start: 0.6944 (mmp) cc_final: 0.6593 (mmm) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.0670 time to fit residues: 24.8478 Evaluate side-chains 215 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 321 ASN A 353 GLN A 355 GLN A 456 GLN B 63 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN B 353 GLN B 355 GLN B 456 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.108438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.092769 restraints weight = 30554.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095063 restraints weight = 21243.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.096731 restraints weight = 16004.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.097981 restraints weight = 12729.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.098986 restraints weight = 10604.689| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8408 Z= 0.201 Angle : 0.686 7.332 11490 Z= 0.362 Chirality : 0.045 0.172 1278 Planarity : 0.006 0.075 1388 Dihedral : 5.875 55.127 1234 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.78 % Allowed : 12.06 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.25), residues: 1016 helix: 0.62 (0.18), residues: 714 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 263 TYR 0.016 0.002 TYR B 137 PHE 0.032 0.002 PHE B 392 TRP 0.025 0.002 TRP A 470 HIS 0.005 0.002 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 8406) covalent geometry : angle 0.68603 (11486) SS BOND : bond 0.00435 ( 2) SS BOND : angle 0.82623 ( 4) hydrogen bonds : bond 0.05260 ( 515) hydrogen bonds : angle 5.11362 ( 1521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8865 (mt) cc_final: 0.8631 (mt) REVERT: A 172 MET cc_start: 0.6674 (ppp) cc_final: 0.6367 (ppp) REVERT: A 173 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 176 MET cc_start: 0.7599 (ppp) cc_final: 0.7187 (ppp) REVERT: A 293 ASP cc_start: 0.8716 (m-30) cc_final: 0.8505 (m-30) REVERT: A 299 PHE cc_start: 0.8129 (m-80) cc_final: 0.7879 (m-80) REVERT: A 327 MET cc_start: 0.8522 (ppp) cc_final: 0.8252 (ppp) REVERT: A 446 MET cc_start: 0.8194 (mmt) cc_final: 0.7605 (mpp) REVERT: A 452 MET cc_start: 0.8336 (tpp) cc_final: 0.7769 (tpp) REVERT: A 455 PHE cc_start: 0.8890 (t80) cc_final: 0.8275 (t80) REVERT: A 495 MET cc_start: 0.7521 (mmp) cc_final: 0.6671 (mmp) REVERT: A 522 PHE cc_start: 0.8369 (m-80) cc_final: 0.8015 (t80) REVERT: B 173 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7058 (mm-30) REVERT: B 176 MET cc_start: 0.7987 (ppp) cc_final: 0.7731 (ppp) REVERT: B 229 LEU cc_start: 0.9433 (mt) cc_final: 0.9229 (mm) REVERT: B 299 PHE cc_start: 0.8053 (m-80) cc_final: 0.7824 (m-80) REVERT: B 321 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7167 (m-40) REVERT: B 483 TYR cc_start: 0.6449 (t80) cc_final: 0.5838 (t80) REVERT: B 495 MET cc_start: 0.7301 (mmp) cc_final: 0.6535 (mmp) outliers start: 24 outliers final: 13 residues processed: 228 average time/residue: 0.0693 time to fit residues: 23.2480 Evaluate side-chains 218 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 456 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN B 353 GLN B 456 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.109036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.093475 restraints weight = 29930.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.095788 restraints weight = 20902.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.097510 restraints weight = 15825.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.098816 restraints weight = 12577.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.099540 restraints weight = 10423.258| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8408 Z= 0.160 Angle : 0.664 7.791 11490 Z= 0.337 Chirality : 0.044 0.209 1278 Planarity : 0.005 0.061 1388 Dihedral : 5.783 54.396 1234 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.44 % Allowed : 16.71 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1016 helix: 0.64 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 263 TYR 0.017 0.002 TYR B 104 PHE 0.025 0.002 PHE B 458 TRP 0.021 0.001 TRP A 470 HIS 0.005 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8406) covalent geometry : angle 0.66373 (11486) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.76279 ( 4) hydrogen bonds : bond 0.04792 ( 515) hydrogen bonds : angle 4.96208 ( 1521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7334 (t60) cc_final: 0.6882 (t60) REVERT: A 104 TYR cc_start: 0.5764 (t80) cc_final: 0.5361 (t80) REVERT: A 172 MET cc_start: 0.6608 (ppp) cc_final: 0.6349 (ppp) REVERT: A 173 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 176 MET cc_start: 0.7749 (ppp) cc_final: 0.7372 (ppp) REVERT: A 293 ASP cc_start: 0.8741 (m-30) cc_final: 0.8517 (m-30) REVERT: A 322 SER cc_start: 0.8580 (m) cc_final: 0.8194 (p) REVERT: A 327 MET cc_start: 0.8572 (ppp) cc_final: 0.8218 (ppp) REVERT: A 355 GLN cc_start: 0.8460 (mp10) cc_final: 0.8036 (mm-40) REVERT: A 452 MET cc_start: 0.8204 (tpp) cc_final: 0.7659 (tpp) REVERT: A 455 PHE cc_start: 0.8860 (t80) cc_final: 0.8303 (t80) REVERT: A 458 PHE cc_start: 0.9142 (m-80) cc_final: 0.8933 (m-80) REVERT: A 495 MET cc_start: 0.6986 (mmp) cc_final: 0.6153 (mmp) REVERT: A 522 PHE cc_start: 0.8413 (m-80) cc_final: 0.8097 (t80) REVERT: A 532 TYR cc_start: 0.6798 (t80) cc_final: 0.6163 (t80) REVERT: B 172 MET cc_start: 0.5536 (ppp) cc_final: 0.5330 (ttt) REVERT: B 254 PHE cc_start: 0.9190 (m-80) cc_final: 0.8862 (m-80) REVERT: B 327 MET cc_start: 0.8623 (ppp) cc_final: 0.8151 (ppp) REVERT: B 328 LEU cc_start: 0.8972 (mt) cc_final: 0.8411 (mt) REVERT: B 446 MET cc_start: 0.8279 (mmt) cc_final: 0.7399 (mpp) REVERT: B 483 TYR cc_start: 0.6446 (t80) cc_final: 0.5805 (t80) REVERT: B 522 PHE cc_start: 0.8471 (m-80) cc_final: 0.8162 (t80) outliers start: 21 outliers final: 13 residues processed: 230 average time/residue: 0.0673 time to fit residues: 23.1230 Evaluate side-chains 228 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 47 optimal weight: 0.0070 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 456 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN B 456 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.108985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.093425 restraints weight = 30077.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.095733 restraints weight = 20951.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.097537 restraints weight = 15787.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.098837 restraints weight = 12473.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.099876 restraints weight = 10334.909| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8408 Z= 0.142 Angle : 0.647 9.076 11490 Z= 0.329 Chirality : 0.043 0.189 1278 Planarity : 0.005 0.051 1388 Dihedral : 5.725 54.252 1234 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.78 % Allowed : 18.79 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1016 helix: 0.64 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 263 TYR 0.024 0.001 TYR B 137 PHE 0.025 0.002 PHE A 431 TRP 0.027 0.001 TRP A 470 HIS 0.004 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8406) covalent geometry : angle 0.64667 (11486) SS BOND : bond 0.00237 ( 2) SS BOND : angle 0.66011 ( 4) hydrogen bonds : bond 0.04535 ( 515) hydrogen bonds : angle 4.77591 ( 1521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7341 (t60) cc_final: 0.7000 (t60) REVERT: A 173 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 176 MET cc_start: 0.7822 (ppp) cc_final: 0.7514 (ppp) REVERT: A 293 ASP cc_start: 0.8735 (m-30) cc_final: 0.8502 (m-30) REVERT: A 454 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8694 (t) REVERT: A 455 PHE cc_start: 0.8831 (t80) cc_final: 0.8488 (t80) REVERT: A 458 PHE cc_start: 0.9155 (m-80) cc_final: 0.8825 (m-80) REVERT: A 495 MET cc_start: 0.7038 (mmp) cc_final: 0.6174 (mmp) REVERT: A 522 PHE cc_start: 0.8425 (m-80) cc_final: 0.8091 (t80) REVERT: A 554 MET cc_start: 0.7175 (mmm) cc_final: 0.6464 (mmm) REVERT: B 254 PHE cc_start: 0.9155 (m-80) cc_final: 0.8796 (m-80) REVERT: B 287 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8137 (t70) REVERT: B 483 TYR cc_start: 0.6385 (t80) cc_final: 0.5749 (t80) REVERT: B 522 PHE cc_start: 0.8424 (m-80) cc_final: 0.8066 (t80) outliers start: 24 outliers final: 13 residues processed: 235 average time/residue: 0.0707 time to fit residues: 24.7087 Evaluate side-chains 221 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 495 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 0.0050 chunk 25 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 456 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN B 456 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.109144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.093485 restraints weight = 29817.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.095910 restraints weight = 20498.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.097738 restraints weight = 15268.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.099119 restraints weight = 12031.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.100202 restraints weight = 9886.777| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8408 Z= 0.138 Angle : 0.692 14.154 11490 Z= 0.345 Chirality : 0.045 0.225 1278 Planarity : 0.005 0.047 1388 Dihedral : 5.786 54.649 1234 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.55 % Allowed : 22.27 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.25), residues: 1016 helix: 0.61 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 263 TYR 0.023 0.001 TYR B 137 PHE 0.025 0.001 PHE A 431 TRP 0.051 0.001 TRP A 470 HIS 0.004 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8406) covalent geometry : angle 0.69166 (11486) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.77684 ( 4) hydrogen bonds : bond 0.04455 ( 515) hydrogen bonds : angle 4.82838 ( 1521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8706 (mt) cc_final: 0.8481 (mt) REVERT: A 65 TRP cc_start: 0.7359 (t60) cc_final: 0.6997 (t60) REVERT: A 172 MET cc_start: 0.6451 (ppp) cc_final: 0.5869 (ttt) REVERT: A 173 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7319 (mm-30) REVERT: A 293 ASP cc_start: 0.8756 (m-30) cc_final: 0.8495 (m-30) REVERT: A 322 SER cc_start: 0.8440 (m) cc_final: 0.8012 (p) REVERT: A 381 MET cc_start: 0.5928 (ttm) cc_final: 0.4905 (tmm) REVERT: A 440 TYR cc_start: 0.8622 (t80) cc_final: 0.8067 (t80) REVERT: A 454 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8674 (t) REVERT: A 455 PHE cc_start: 0.8876 (t80) cc_final: 0.8553 (t80) REVERT: A 458 PHE cc_start: 0.9205 (m-80) cc_final: 0.8835 (m-80) REVERT: A 483 TYR cc_start: 0.6979 (t80) cc_final: 0.6408 (t80) REVERT: A 495 MET cc_start: 0.7033 (mmp) cc_final: 0.6121 (mmp) REVERT: A 522 PHE cc_start: 0.8423 (m-80) cc_final: 0.8109 (t80) REVERT: B 86 PHE cc_start: 0.8931 (m-80) cc_final: 0.8683 (m-10) REVERT: B 287 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8159 (t70) REVERT: B 440 TYR cc_start: 0.8621 (t80) cc_final: 0.8088 (t80) REVERT: B 483 TYR cc_start: 0.6430 (t80) cc_final: 0.5702 (t80) outliers start: 22 outliers final: 9 residues processed: 226 average time/residue: 0.0686 time to fit residues: 23.3357 Evaluate side-chains 218 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 511 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 456 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN B 456 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.108498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093014 restraints weight = 29369.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.095433 restraints weight = 19990.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.097024 restraints weight = 14713.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.098344 restraints weight = 11856.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.099643 restraints weight = 9751.051| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8408 Z= 0.141 Angle : 0.698 10.995 11490 Z= 0.348 Chirality : 0.045 0.208 1278 Planarity : 0.004 0.046 1388 Dihedral : 5.765 53.333 1234 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.20 % Allowed : 24.59 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1016 helix: 0.66 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 263 TYR 0.021 0.001 TYR B 137 PHE 0.033 0.002 PHE B 79 TRP 0.020 0.001 TRP B 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8406) covalent geometry : angle 0.69770 (11486) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.61359 ( 4) hydrogen bonds : bond 0.04383 ( 515) hydrogen bonds : angle 4.81766 ( 1521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8718 (mt) cc_final: 0.8295 (mt) REVERT: A 65 TRP cc_start: 0.7365 (t60) cc_final: 0.7042 (t60) REVERT: A 69 TYR cc_start: 0.7868 (t80) cc_final: 0.7651 (t80) REVERT: A 73 LYS cc_start: 0.8722 (ptmm) cc_final: 0.8289 (ptmm) REVERT: A 104 TYR cc_start: 0.6034 (t80) cc_final: 0.5720 (t80) REVERT: A 173 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 287 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8142 (t70) REVERT: A 293 ASP cc_start: 0.8742 (m-30) cc_final: 0.8448 (m-30) REVERT: A 324 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7341 (ptt90) REVERT: A 327 MET cc_start: 0.9218 (ptp) cc_final: 0.8578 (ppp) REVERT: A 454 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.8738 (t) REVERT: A 455 PHE cc_start: 0.8844 (t80) cc_final: 0.8530 (t80) REVERT: A 458 PHE cc_start: 0.9199 (m-80) cc_final: 0.8859 (m-80) REVERT: A 495 MET cc_start: 0.7007 (mmp) cc_final: 0.6044 (mmp) REVERT: A 522 PHE cc_start: 0.8462 (m-80) cc_final: 0.8124 (t80) REVERT: B 86 PHE cc_start: 0.8931 (m-80) cc_final: 0.8682 (m-10) REVERT: B 172 MET cc_start: 0.7081 (ppp) cc_final: 0.6340 (ttp) REVERT: B 254 PHE cc_start: 0.9152 (m-80) cc_final: 0.8858 (m-80) REVERT: B 287 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8337 (t0) REVERT: B 327 MET cc_start: 0.8889 (ptm) cc_final: 0.8468 (ptp) REVERT: B 483 TYR cc_start: 0.6252 (t80) cc_final: 0.5596 (t80) REVERT: B 522 PHE cc_start: 0.8435 (m-80) cc_final: 0.8085 (t80) outliers start: 19 outliers final: 10 residues processed: 228 average time/residue: 0.0709 time to fit residues: 23.9736 Evaluate side-chains 218 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 495 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 456 GLN ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.109388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.093468 restraints weight = 29798.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.095945 restraints weight = 20438.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.097782 restraints weight = 15220.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.099207 restraints weight = 11991.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.099936 restraints weight = 9795.821| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8408 Z= 0.148 Angle : 0.752 19.189 11490 Z= 0.366 Chirality : 0.046 0.240 1278 Planarity : 0.004 0.046 1388 Dihedral : 5.747 52.856 1234 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.44 % Allowed : 28.19 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.26), residues: 1016 helix: 0.52 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.47 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 263 TYR 0.026 0.002 TYR A 440 PHE 0.027 0.002 PHE B 79 TRP 0.019 0.001 TRP B 470 HIS 0.003 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8406) covalent geometry : angle 0.75194 (11486) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.53341 ( 4) hydrogen bonds : bond 0.04412 ( 515) hydrogen bonds : angle 4.89878 ( 1521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7373 (t60) cc_final: 0.7057 (t60) REVERT: A 73 LYS cc_start: 0.8661 (ptmm) cc_final: 0.8223 (ptmm) REVERT: A 104 TYR cc_start: 0.5899 (t80) cc_final: 0.5692 (t80) REVERT: A 287 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8289 (t70) REVERT: A 293 ASP cc_start: 0.8786 (m-30) cc_final: 0.8499 (m-30) REVERT: A 324 ARG cc_start: 0.7688 (mmt90) cc_final: 0.7365 (ptt90) REVERT: A 327 MET cc_start: 0.9183 (ptp) cc_final: 0.8514 (ppp) REVERT: A 381 MET cc_start: 0.5666 (ttm) cc_final: 0.4908 (tmm) REVERT: A 410 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8875 (pm20) REVERT: A 454 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.8809 (t) REVERT: A 455 PHE cc_start: 0.8831 (t80) cc_final: 0.8524 (t80) REVERT: A 458 PHE cc_start: 0.9226 (m-80) cc_final: 0.8972 (m-80) REVERT: A 483 TYR cc_start: 0.6916 (t80) cc_final: 0.6229 (t80) REVERT: A 495 MET cc_start: 0.7183 (mmp) cc_final: 0.6215 (mmp) REVERT: A 522 PHE cc_start: 0.8431 (m-80) cc_final: 0.8112 (t80) REVERT: B 86 PHE cc_start: 0.8930 (m-80) cc_final: 0.8708 (m-10) REVERT: B 172 MET cc_start: 0.7327 (ppp) cc_final: 0.6346 (ttp) REVERT: B 228 TRP cc_start: 0.7808 (m100) cc_final: 0.7476 (m100) REVERT: B 327 MET cc_start: 0.8866 (ptm) cc_final: 0.8524 (ptp) REVERT: B 410 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: B 483 TYR cc_start: 0.6184 (t80) cc_final: 0.5458 (t80) REVERT: B 522 PHE cc_start: 0.8477 (m-80) cc_final: 0.8107 (t80) outliers start: 21 outliers final: 12 residues processed: 231 average time/residue: 0.0718 time to fit residues: 24.6885 Evaluate side-chains 222 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 470 TRP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 511 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 61 optimal weight: 0.0030 chunk 36 optimal weight: 0.0050 chunk 96 optimal weight: 0.6980 chunk 75 optimal weight: 0.0050 overall best weight: 0.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** B 355 GLN ** 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 = 0.4105 r_free = 0.4105 target = 0.111514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.095636 restraints weight = 29253.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.098109 restraints weight = 20056.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.099724 restraints weight = 14939.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.101293 restraints weight = 12013.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.102485 restraints weight = 9742.513| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8408 Z= 0.143 Angle : 0.768 12.095 11490 Z= 0.375 Chirality : 0.047 0.252 1278 Planarity : 0.004 0.044 1388 Dihedral : 5.774 55.202 1234 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.32 % Allowed : 28.31 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.25), residues: 1016 helix: 0.52 (0.19), residues: 714 sheet: None (None), residues: 0 loop : -0.42 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 263 TYR 0.022 0.001 TYR B 137 PHE 0.028 0.002 PHE B 79 TRP 0.018 0.001 TRP B 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8406) covalent geometry : angle 0.76821 (11486) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.50014 ( 4) hydrogen bonds : bond 0.04362 ( 515) hydrogen bonds : angle 4.86541 ( 1521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8701 (mt) cc_final: 0.8247 (mt) REVERT: A 65 TRP cc_start: 0.7321 (t60) cc_final: 0.7108 (t60) REVERT: A 69 TYR cc_start: 0.8240 (t80) cc_final: 0.7857 (t80) REVERT: A 71 CYS cc_start: 0.9155 (t) cc_final: 0.8918 (t) REVERT: A 96 PHE cc_start: 0.8739 (t80) cc_final: 0.8476 (t80) REVERT: A 104 TYR cc_start: 0.5818 (t80) cc_final: 0.5605 (t80) REVERT: A 228 TRP cc_start: 0.8008 (m100) cc_final: 0.7792 (m100) REVERT: A 287 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8251 (t70) REVERT: A 293 ASP cc_start: 0.8785 (m-30) cc_final: 0.8435 (m-30) REVERT: A 309 MET cc_start: 0.6721 (mmm) cc_final: 0.6433 (mmm) REVERT: A 324 ARG cc_start: 0.7563 (mmt90) cc_final: 0.7284 (ptt90) REVERT: A 327 MET cc_start: 0.9030 (ptp) cc_final: 0.8553 (ppp) REVERT: A 381 MET cc_start: 0.5259 (ttm) cc_final: 0.4444 (tmm) REVERT: A 410 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8879 (pm20) REVERT: A 434 PHE cc_start: 0.8274 (t80) cc_final: 0.8064 (t80) REVERT: A 446 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7902 (mpp) REVERT: A 454 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8540 (t) REVERT: A 455 PHE cc_start: 0.8822 (t80) cc_final: 0.8574 (t80) REVERT: A 458 PHE cc_start: 0.9245 (m-80) cc_final: 0.8988 (m-80) REVERT: A 483 TYR cc_start: 0.6793 (t80) cc_final: 0.6452 (t80) REVERT: A 495 MET cc_start: 0.7176 (mmp) cc_final: 0.6249 (mmp) REVERT: A 522 PHE cc_start: 0.8409 (m-80) cc_final: 0.8193 (t80) REVERT: B 71 CYS cc_start: 0.9097 (t) cc_final: 0.8799 (t) REVERT: B 86 PHE cc_start: 0.8941 (m-80) cc_final: 0.8731 (m-10) REVERT: B 172 MET cc_start: 0.7332 (ppp) cc_final: 0.6239 (ttp) REVERT: B 327 MET cc_start: 0.8846 (ptm) cc_final: 0.8464 (ptp) REVERT: B 381 MET cc_start: 0.4736 (ttm) cc_final: 0.4407 (tmm) REVERT: B 410 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8754 (pm20) REVERT: B 483 TYR cc_start: 0.6346 (t80) cc_final: 0.5554 (t80) REVERT: B 495 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6237 (mmp) REVERT: B 522 PHE cc_start: 0.8448 (m-80) cc_final: 0.8095 (t80) outliers start: 20 outliers final: 5 residues processed: 233 average time/residue: 0.0710 time to fit residues: 24.6170 Evaluate side-chains 223 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 495 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.0050 chunk 64 optimal weight: 0.0170 chunk 100 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 overall best weight: 1.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 456 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.109182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.093039 restraints weight = 29292.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.095388 restraints weight = 20428.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.097168 restraints weight = 15431.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.098610 restraints weight = 12496.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.099680 restraints weight = 10162.725| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8408 Z= 0.158 Angle : 0.872 17.526 11490 Z= 0.409 Chirality : 0.049 0.250 1278 Planarity : 0.005 0.047 1388 Dihedral : 5.828 53.883 1234 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.32 % Allowed : 29.47 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1016 helix: 0.41 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.43 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 263 TYR 0.022 0.002 TYR A 440 PHE 0.027 0.002 PHE A 431 TRP 0.053 0.001 TRP B 470 HIS 0.002 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8406) covalent geometry : angle 0.87237 (11486) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.51464 ( 4) hydrogen bonds : bond 0.04444 ( 515) hydrogen bonds : angle 4.99465 ( 1521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8647 (mt) cc_final: 0.8428 (mt) REVERT: A 65 TRP cc_start: 0.7508 (t60) cc_final: 0.7138 (t60) REVERT: A 69 TYR cc_start: 0.8335 (t80) cc_final: 0.8040 (t80) REVERT: A 71 CYS cc_start: 0.9205 (t) cc_final: 0.8956 (t) REVERT: A 287 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8405 (t70) REVERT: A 293 ASP cc_start: 0.8827 (m-30) cc_final: 0.8606 (m-30) REVERT: A 309 MET cc_start: 0.6723 (mmm) cc_final: 0.6467 (mmm) REVERT: A 342 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.9059 (t80) REVERT: A 381 MET cc_start: 0.5519 (ttm) cc_final: 0.4654 (tmm) REVERT: A 410 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8921 (pm20) REVERT: A 434 PHE cc_start: 0.8260 (t80) cc_final: 0.8057 (t80) REVERT: A 446 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: A 454 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 458 PHE cc_start: 0.9248 (m-80) cc_final: 0.9031 (m-80) REVERT: A 483 TYR cc_start: 0.6801 (t80) cc_final: 0.6439 (t80) REVERT: A 495 MET cc_start: 0.7238 (mmp) cc_final: 0.6302 (mmp) REVERT: A 522 PHE cc_start: 0.8363 (m-80) cc_final: 0.8024 (t80) REVERT: B 86 PHE cc_start: 0.8982 (m-80) cc_final: 0.8777 (m-10) REVERT: B 172 MET cc_start: 0.7557 (ppp) cc_final: 0.6304 (ttp) REVERT: B 254 PHE cc_start: 0.9191 (m-80) cc_final: 0.8865 (m-80) REVERT: B 327 MET cc_start: 0.8842 (ptm) cc_final: 0.8497 (ptp) REVERT: B 410 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8785 (pm20) REVERT: B 483 TYR cc_start: 0.6349 (t80) cc_final: 0.5561 (t80) REVERT: B 495 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6323 (mmp) REVERT: B 522 PHE cc_start: 0.8490 (m-80) cc_final: 0.8127 (t80) outliers start: 20 outliers final: 8 residues processed: 224 average time/residue: 0.0703 time to fit residues: 23.5106 Evaluate side-chains 226 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 495 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 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 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.110782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094534 restraints weight = 28925.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.096977 restraints weight = 20135.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.098842 restraints weight = 15141.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.100266 restraints weight = 12011.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.101373 restraints weight = 9867.608| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8408 Z= 0.152 Angle : 0.911 20.773 11490 Z= 0.423 Chirality : 0.049 0.246 1278 Planarity : 0.005 0.049 1388 Dihedral : 5.809 53.795 1234 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.97 % Allowed : 30.28 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.25), residues: 1016 helix: 0.37 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.38 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 263 TYR 0.023 0.001 TYR A 440 PHE 0.029 0.002 PHE A 431 TRP 0.081 0.002 TRP B 470 HIS 0.003 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8406) covalent geometry : angle 0.91139 (11486) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.53429 ( 4) hydrogen bonds : bond 0.04510 ( 515) hydrogen bonds : angle 5.03599 ( 1521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8647 (mt) cc_final: 0.8421 (mt) REVERT: A 65 TRP cc_start: 0.7502 (t60) cc_final: 0.7140 (t60) REVERT: A 69 TYR cc_start: 0.8315 (t80) cc_final: 0.8084 (t80) REVERT: A 71 CYS cc_start: 0.9180 (t) cc_final: 0.8925 (t) REVERT: A 228 TRP cc_start: 0.7971 (m100) cc_final: 0.7758 (m100) REVERT: A 287 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8371 (t70) REVERT: A 293 ASP cc_start: 0.8824 (m-30) cc_final: 0.8608 (m-30) REVERT: A 322 SER cc_start: 0.8763 (m) cc_final: 0.8424 (p) REVERT: A 342 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.9044 (t80) REVERT: A 381 MET cc_start: 0.5404 (ttm) cc_final: 0.4555 (tmm) REVERT: A 410 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8904 (pm20) REVERT: A 454 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.8701 (t) REVERT: A 455 PHE cc_start: 0.8838 (t80) cc_final: 0.8590 (t80) REVERT: A 458 PHE cc_start: 0.9239 (m-80) cc_final: 0.8942 (m-80) REVERT: A 483 TYR cc_start: 0.6811 (t80) cc_final: 0.6520 (t80) REVERT: A 495 MET cc_start: 0.7103 (mmp) cc_final: 0.6168 (mmp) REVERT: A 504 MET cc_start: 0.8529 (mtm) cc_final: 0.8202 (mpp) REVERT: A 522 PHE cc_start: 0.8324 (m-80) cc_final: 0.7968 (t80) REVERT: B 172 MET cc_start: 0.7515 (ppp) cc_final: 0.6269 (ttp) REVERT: B 254 PHE cc_start: 0.9168 (m-80) cc_final: 0.8828 (m-80) REVERT: B 327 MET cc_start: 0.8835 (ptm) cc_final: 0.8495 (ptp) REVERT: B 410 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: B 483 TYR cc_start: 0.6327 (t80) cc_final: 0.5464 (t80) REVERT: B 495 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6256 (mmp) REVERT: B 522 PHE cc_start: 0.8487 (m-80) cc_final: 0.8166 (t80) outliers start: 17 outliers final: 7 residues processed: 224 average time/residue: 0.0698 time to fit residues: 23.6336 Evaluate side-chains 225 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 495 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 31 optimal weight: 0.0040 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.111175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.095438 restraints weight = 29023.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.097833 restraints weight = 20275.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.099554 restraints weight = 15275.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.100929 restraints weight = 12159.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.101973 restraints weight = 10040.714| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8408 Z= 0.150 Angle : 0.904 18.425 11490 Z= 0.423 Chirality : 0.049 0.243 1278 Planarity : 0.005 0.049 1388 Dihedral : 5.797 55.037 1234 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.20 % Allowed : 30.28 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.25), residues: 1016 helix: 0.39 (0.19), residues: 714 sheet: None (None), residues: 0 loop : -0.24 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 263 TYR 0.026 0.001 TYR A 440 PHE 0.029 0.002 PHE A 431 TRP 0.031 0.001 TRP B 228 HIS 0.003 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8406) covalent geometry : angle 0.90415 (11486) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.46205 ( 4) hydrogen bonds : bond 0.04483 ( 515) hydrogen bonds : angle 5.01300 ( 1521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1357.64 seconds wall clock time: 24 minutes 20.41 seconds (1460.41 seconds total)