Starting phenix.real_space_refine on Sat Jul 26 07:21:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdl_61395/07_2025/9jdl_61395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdl_61395/07_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_61395/07_2025/9jdl_61395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdl_61395/07_2025/9jdl_61395.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdl_61395/07_2025/9jdl_61395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdl_61395/07_2025/9jdl_61395_neut.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.67, per 1000 atoms: 0.70 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: 2.35 Conformation dependent library (CDL) restraints added in 911.8 milliseconds 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: 0.97 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: 2.50 Time building geometry restraints manager: 2.72 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: 0.04 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: 45.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (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 TRP 0.013 0.001 TRP B 65 HIS 0.001 0.001 HIS B 161 PHE 0.015 0.001 PHE A 458 TYR 0.016 0.001 TYR B 137 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.25585 ( 515) hydrogen bonds : angle 7.68395 ( 1521) SS BOND : bond 0.00360 ( 2) SS BOND : angle 1.49932 ( 4) covalent geometry : bond 0.00324 ( 8406) covalent geometry : angle 0.57758 (11486) *********************** 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 : 0.807 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: 0.7518 (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: 0.6643 (t80) REVERT: B 104 TYR cc_start: 0.5641 (t80) cc_final: 0.5408 (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: 0.7768 (m-80) REVERT: B 302 TYR cc_start: 0.7788 (m-80) cc_final: 0.6954 (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: 0.7945 (ppp) REVERT: B 328 LEU cc_start: 0.8839 (mt) cc_final: 0.8372 (mt) REVERT: B 334 SER cc_start: 0.8025 (p) cc_final: 0.7715 (p) 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: 0.6592 (mmm) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.1523 time to fit residues: 55.1287 Evaluate side-chains 214 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.2980 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 353 GLN A 355 GLN A 456 GLN B 63 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN B 355 GLN B 456 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.112364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.096427 restraints weight = 29458.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.098835 restraints weight = 20540.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100455 restraints weight = 15443.389| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8408 Z= 0.159 Angle : 0.667 7.760 11490 Z= 0.347 Chirality : 0.044 0.167 1278 Planarity : 0.006 0.073 1388 Dihedral : 5.818 59.147 1234 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.55 % Allowed : 11.48 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1016 helix: 0.61 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -0.62 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 470 HIS 0.007 0.002 HIS B 170 PHE 0.032 0.002 PHE A 79 TYR 0.019 0.002 TYR B 137 ARG 0.007 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.05366 ( 515) hydrogen bonds : angle 5.05385 ( 1521) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.92826 ( 4) covalent geometry : bond 0.00355 ( 8406) covalent geometry : angle 0.66715 (11486) *********************** 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 252 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8797 (mt) cc_final: 0.8588 (mt) REVERT: A 172 MET cc_start: 0.6523 (ppp) cc_final: 0.6205 (ppp) REVERT: A 176 MET cc_start: 0.7832 (ppp) cc_final: 0.7423 (ppp) REVERT: A 358 ASP cc_start: 0.8875 (p0) cc_final: 0.8639 (p0) REVERT: A 380 MET cc_start: 0.8792 (mmp) cc_final: 0.8592 (mmm) REVERT: A 452 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7869 (tpp) REVERT: A 455 PHE cc_start: 0.8801 (t80) cc_final: 0.8205 (t80) REVERT: A 483 TYR cc_start: 0.6967 (t80) cc_final: 0.6479 (t80) REVERT: A 495 MET cc_start: 0.7337 (mmp) cc_final: 0.6606 (mmp) REVERT: A 522 PHE cc_start: 0.8334 (m-80) cc_final: 0.8116 (t80) REVERT: B 104 TYR cc_start: 0.5943 (t80) cc_final: 0.5700 (t80) REVERT: B 176 MET cc_start: 0.7992 (ppp) cc_final: 0.7774 (ppp) REVERT: B 224 LEU cc_start: 0.9393 (tp) cc_final: 0.8961 (tp) REVERT: B 229 LEU cc_start: 0.9455 (mt) cc_final: 0.9248 (mm) REVERT: B 327 MET cc_start: 0.8494 (ppp) cc_final: 0.8017 (ppp) REVERT: B 328 LEU cc_start: 0.8932 (mt) cc_final: 0.8369 (mt) REVERT: B 440 TYR cc_start: 0.8486 (t80) cc_final: 0.7879 (t80) REVERT: B 461 TYR cc_start: 0.7370 (m-80) cc_final: 0.6921 (m-80) REVERT: B 483 TYR cc_start: 0.6474 (t80) cc_final: 0.5764 (t80) REVERT: B 495 MET cc_start: 0.7182 (mmp) cc_final: 0.6543 (mmp) outliers start: 22 outliers final: 11 residues processed: 240 average time/residue: 0.1644 time to fit residues: 56.7682 Evaluate side-chains 223 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 353 GLN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 452 MET 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 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 88 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.109313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.093387 restraints weight = 30193.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.095505 restraints weight = 21442.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.097237 restraints weight = 16567.477| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8408 Z= 0.171 Angle : 0.681 13.031 11490 Z= 0.344 Chirality : 0.044 0.181 1278 Planarity : 0.005 0.061 1388 Dihedral : 5.823 57.245 1234 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.67 % Allowed : 15.55 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1016 helix: 0.69 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 144 HIS 0.004 0.001 HIS B 170 PHE 0.025 0.002 PHE B 431 TYR 0.013 0.002 TYR B 374 ARG 0.007 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 515) hydrogen bonds : angle 4.92814 ( 1521) SS BOND : bond 0.00341 ( 2) SS BOND : angle 0.73598 ( 4) covalent geometry : bond 0.00380 ( 8406) covalent geometry : angle 0.68105 (11486) *********************** 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 234 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7260 (t60) cc_final: 0.6889 (t60) REVERT: A 73 LYS cc_start: 0.8667 (ptmm) cc_final: 0.8416 (ptmm) REVERT: A 104 TYR cc_start: 0.5538 (t80) cc_final: 0.5169 (t80) REVERT: A 172 MET cc_start: 0.6633 (ppp) cc_final: 0.6241 (ppp) REVERT: A 176 MET cc_start: 0.8002 (ppp) cc_final: 0.7524 (ppp) REVERT: A 256 MET cc_start: 0.7557 (mtp) cc_final: 0.7329 (mtp) REVERT: A 293 ASP cc_start: 0.8573 (m-30) cc_final: 0.8249 (m-30) REVERT: A 452 MET cc_start: 0.8371 (tpp) cc_final: 0.7920 (tpp) REVERT: A 455 PHE cc_start: 0.8694 (t80) cc_final: 0.8358 (t80) REVERT: A 458 PHE cc_start: 0.9098 (m-80) cc_final: 0.8828 (m-80) REVERT: A 495 MET cc_start: 0.7148 (mmp) cc_final: 0.6315 (mmp) REVERT: B 321 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7126 (m-40) REVERT: B 437 SER cc_start: 0.8800 (t) cc_final: 0.8446 (p) REVERT: B 446 MET cc_start: 0.8322 (mmt) cc_final: 0.7424 (mpp) REVERT: B 461 TYR cc_start: 0.7326 (m-80) cc_final: 0.6810 (m-80) REVERT: B 483 TYR cc_start: 0.6381 (t80) cc_final: 0.5756 (t80) REVERT: B 495 MET cc_start: 0.7237 (mmp) cc_final: 0.6899 (mmp) outliers start: 23 outliers final: 9 residues processed: 224 average time/residue: 0.2059 time to fit residues: 67.2813 Evaluate side-chains 212 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 287 ASP Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 446 MET 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 321 ASN 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 85 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.109866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.093696 restraints weight = 29012.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.096139 restraints weight = 20018.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.097980 restraints weight = 14962.303| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8408 Z= 0.144 Angle : 0.680 10.331 11490 Z= 0.339 Chirality : 0.044 0.246 1278 Planarity : 0.005 0.053 1388 Dihedral : 5.797 57.893 1234 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.20 % Allowed : 19.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1016 helix: 0.68 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 470 HIS 0.004 0.001 HIS B 170 PHE 0.026 0.002 PHE B 431 TYR 0.019 0.001 TYR B 104 ARG 0.008 0.001 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 515) hydrogen bonds : angle 4.80621 ( 1521) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.67939 ( 4) covalent geometry : bond 0.00318 ( 8406) covalent geometry : angle 0.67982 (11486) *********************** 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 233 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.5685 (t80) cc_final: 0.5281 (t80) REVERT: A 176 MET cc_start: 0.7950 (ppp) cc_final: 0.7643 (ppp) REVERT: A 293 ASP cc_start: 0.8722 (m-30) cc_final: 0.8504 (m-30) REVERT: A 353 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7892 (pp30) REVERT: A 452 MET cc_start: 0.8427 (tpp) cc_final: 0.8089 (tpp) REVERT: A 454 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8596 (t) REVERT: A 455 PHE cc_start: 0.8837 (t80) cc_final: 0.8467 (t80) REVERT: A 458 PHE cc_start: 0.9226 (m-80) cc_final: 0.8757 (m-80) REVERT: A 483 TYR cc_start: 0.7017 (t80) cc_final: 0.6418 (t80) REVERT: A 495 MET cc_start: 0.6950 (mmp) cc_final: 0.6063 (mmp) REVERT: A 522 PHE cc_start: 0.8360 (m-80) cc_final: 0.7976 (t80) REVERT: A 532 TYR cc_start: 0.6860 (t80) cc_final: 0.6402 (t80) REVERT: B 176 MET cc_start: 0.7865 (ppp) cc_final: 0.7568 (ppp) REVERT: B 254 PHE cc_start: 0.9168 (m-80) cc_final: 0.8824 (m-80) REVERT: B 446 MET cc_start: 0.8337 (mmt) cc_final: 0.7545 (mpp) REVERT: B 458 PHE cc_start: 0.9279 (m-80) cc_final: 0.9041 (m-80) REVERT: B 461 TYR cc_start: 0.7269 (m-80) cc_final: 0.6706 (m-80) REVERT: B 483 TYR cc_start: 0.6425 (t80) cc_final: 0.5735 (t80) REVERT: B 522 PHE cc_start: 0.8377 (m-80) cc_final: 0.8015 (t80) outliers start: 19 outliers final: 9 residues processed: 222 average time/residue: 0.2056 time to fit residues: 66.9399 Evaluate side-chains 220 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 353 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 456 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.108325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.092542 restraints weight = 29268.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.094853 restraints weight = 20268.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.096646 restraints weight = 15279.364| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8408 Z= 0.147 Angle : 0.693 14.102 11490 Z= 0.341 Chirality : 0.044 0.175 1278 Planarity : 0.004 0.046 1388 Dihedral : 5.820 56.193 1234 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.97 % Allowed : 21.46 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1016 helix: 0.74 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.032 0.002 PHE A 299 TYR 0.010 0.001 TYR B 483 ARG 0.008 0.001 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 515) hydrogen bonds : angle 4.72005 ( 1521) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.66077 ( 4) covalent geometry : bond 0.00333 ( 8406) covalent geometry : angle 0.69260 (11486) *********************** 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 234 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7371 (t60) cc_final: 0.6940 (t60) REVERT: A 172 MET cc_start: 0.6589 (ppp) cc_final: 0.6114 (ttt) REVERT: A 293 ASP cc_start: 0.8694 (m-30) cc_final: 0.8477 (m-30) REVERT: A 455 PHE cc_start: 0.8802 (t80) cc_final: 0.8509 (t80) REVERT: A 458 PHE cc_start: 0.9240 (m-80) cc_final: 0.8876 (m-80) REVERT: A 495 MET cc_start: 0.6997 (mmp) cc_final: 0.6045 (mmp) REVERT: A 522 PHE cc_start: 0.8400 (m-80) cc_final: 0.7999 (t80) REVERT: A 532 TYR cc_start: 0.6848 (t80) cc_final: 0.6463 (t80) REVERT: B 86 PHE cc_start: 0.8926 (m-80) cc_final: 0.8695 (m-10) REVERT: B 139 ILE cc_start: 0.9513 (tp) cc_final: 0.9130 (tp) REVERT: B 228 TRP cc_start: 0.7954 (m100) cc_final: 0.7715 (m100) REVERT: B 254 PHE cc_start: 0.9174 (m-80) cc_final: 0.8828 (m-80) REVERT: B 287 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8150 (t70) REVERT: B 351 MET cc_start: 0.9333 (ptp) cc_final: 0.9047 (ptp) REVERT: B 446 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7698 (mpp) REVERT: B 452 MET cc_start: 0.8144 (tpp) cc_final: 0.7595 (tpp) REVERT: B 458 PHE cc_start: 0.9240 (m-80) cc_final: 0.8934 (m-80) REVERT: B 483 TYR cc_start: 0.6430 (t80) cc_final: 0.5776 (t80) REVERT: B 495 MET cc_start: 0.7169 (mmp) cc_final: 0.6510 (mmp) outliers start: 17 outliers final: 9 residues processed: 225 average time/residue: 0.2008 time to fit residues: 66.6765 Evaluate side-chains 221 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 298 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 446 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.108154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.092695 restraints weight = 29193.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.095096 restraints weight = 19969.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.096828 restraints weight = 14867.048| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3351 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= 0.141 Angle : 0.703 12.311 11490 Z= 0.344 Chirality : 0.045 0.187 1278 Planarity : 0.004 0.045 1388 Dihedral : 5.771 54.580 1234 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.97 % Allowed : 23.55 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1016 helix: 0.75 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -0.65 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.033 0.002 PHE B 79 TYR 0.012 0.001 TYR A 104 ARG 0.008 0.001 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 515) hydrogen bonds : angle 4.76182 ( 1521) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.68214 ( 4) covalent geometry : bond 0.00320 ( 8406) covalent geometry : angle 0.70308 (11486) *********************** 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 240 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8705 (mt) cc_final: 0.8501 (mt) REVERT: A 65 TRP cc_start: 0.7294 (t60) cc_final: 0.6977 (t60) REVERT: A 69 TYR cc_start: 0.7697 (t80) cc_final: 0.7466 (t80) REVERT: A 172 MET cc_start: 0.6646 (ppp) cc_final: 0.6442 (ppp) REVERT: A 256 MET cc_start: 0.7914 (mtp) cc_final: 0.7667 (mtp) REVERT: A 293 ASP cc_start: 0.8705 (m-30) cc_final: 0.8480 (m-30) REVERT: A 353 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7947 (pp30) REVERT: A 381 MET cc_start: 0.5913 (ttm) cc_final: 0.5063 (tmm) REVERT: A 440 TYR cc_start: 0.8603 (t80) cc_final: 0.8260 (t80) REVERT: A 454 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.8537 (t) REVERT: A 455 PHE cc_start: 0.8777 (t80) cc_final: 0.8493 (t80) REVERT: A 458 PHE cc_start: 0.9255 (m-80) cc_final: 0.8799 (m-80) REVERT: A 483 TYR cc_start: 0.6919 (t80) cc_final: 0.6395 (t80) REVERT: A 495 MET cc_start: 0.7022 (mmp) cc_final: 0.6052 (mmp) REVERT: A 522 PHE cc_start: 0.8397 (m-80) cc_final: 0.7953 (t80) REVERT: B 86 PHE cc_start: 0.8915 (m-80) cc_final: 0.8692 (m-10) REVERT: B 139 ILE cc_start: 0.9516 (tp) cc_final: 0.8747 (tp) REVERT: B 228 TRP cc_start: 0.7882 (m100) cc_final: 0.7572 (m100) REVERT: B 254 PHE cc_start: 0.9198 (m-80) cc_final: 0.8705 (m-80) REVERT: B 287 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8177 (t0) REVERT: B 446 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7418 (mpp) REVERT: B 452 MET cc_start: 0.8172 (tpp) cc_final: 0.7651 (tpp) REVERT: B 458 PHE cc_start: 0.9277 (m-80) cc_final: 0.8990 (m-80) REVERT: B 483 TYR cc_start: 0.6289 (t80) cc_final: 0.5606 (t80) REVERT: B 495 MET cc_start: 0.7220 (mmp) cc_final: 0.6429 (mmp) REVERT: B 522 PHE cc_start: 0.8445 (m-80) cc_final: 0.7975 (t80) outliers start: 17 outliers final: 8 residues processed: 231 average time/residue: 0.2404 time to fit residues: 81.4020 Evaluate side-chains 227 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 204 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.0070 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.109508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.094044 restraints weight = 29418.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.096367 restraints weight = 20486.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.098029 restraints weight = 15388.750| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8408 Z= 0.137 Angle : 0.724 13.873 11490 Z= 0.353 Chirality : 0.045 0.307 1278 Planarity : 0.005 0.042 1388 Dihedral : 5.767 55.519 1234 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.78 % Allowed : 25.29 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1016 helix: 0.75 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.54 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 PHE 0.043 0.002 PHE A 299 TYR 0.014 0.001 TYR A 461 ARG 0.007 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 515) hydrogen bonds : angle 4.74128 ( 1521) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.53149 ( 4) covalent geometry : bond 0.00310 ( 8406) covalent geometry : angle 0.72408 (11486) *********************** 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 249 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7199 (t60) cc_final: 0.6898 (t60) REVERT: A 69 TYR cc_start: 0.7788 (t80) cc_final: 0.7520 (t80) REVERT: A 71 CYS cc_start: 0.9109 (t) cc_final: 0.8907 (t) REVERT: A 172 MET cc_start: 0.6665 (ppp) cc_final: 0.6150 (ttt) REVERT: A 287 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7974 (t70) REVERT: A 353 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7886 (pp30) REVERT: A 410 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8921 (pm20) REVERT: A 440 TYR cc_start: 0.8501 (t80) cc_final: 0.8072 (t80) REVERT: A 454 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.8501 (t) REVERT: A 455 PHE cc_start: 0.8692 (t80) cc_final: 0.8487 (t80) REVERT: A 458 PHE cc_start: 0.9257 (m-80) cc_final: 0.8871 (m-80) REVERT: A 483 TYR cc_start: 0.6933 (t80) cc_final: 0.6609 (t80) REVERT: A 495 MET cc_start: 0.7153 (mmp) cc_final: 0.6213 (mmp) REVERT: A 504 MET cc_start: 0.8660 (mtm) cc_final: 0.7864 (mtm) REVERT: A 522 PHE cc_start: 0.8418 (m-80) cc_final: 0.8035 (t80) REVERT: B 86 PHE cc_start: 0.8888 (m-80) cc_final: 0.8662 (m-10) REVERT: B 139 ILE cc_start: 0.9490 (tp) cc_final: 0.8680 (tp) REVERT: B 172 MET cc_start: 0.7060 (ppp) cc_final: 0.6119 (ttp) REVERT: B 228 TRP cc_start: 0.7833 (m100) cc_final: 0.7553 (m100) REVERT: B 287 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8287 (t0) REVERT: B 446 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7373 (mpp) REVERT: B 452 MET cc_start: 0.8033 (tpp) cc_final: 0.7431 (tpp) REVERT: B 454 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.8463 (t) REVERT: B 458 PHE cc_start: 0.9243 (m-80) cc_final: 0.8956 (m-80) REVERT: B 483 TYR cc_start: 0.6291 (t80) cc_final: 0.5557 (t80) REVERT: B 495 MET cc_start: 0.7362 (mmp) cc_final: 0.6561 (mmp) REVERT: B 522 PHE cc_start: 0.8423 (m-80) cc_final: 0.7960 (t80) REVERT: B 554 MET cc_start: 0.6619 (mmm) cc_final: 0.5712 (mmm) outliers start: 24 outliers final: 9 residues processed: 237 average time/residue: 0.1743 time to fit residues: 61.5411 Evaluate side-chains 227 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 410 GLN 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 204 LEU Chi-restraints excluded: chain B residue 256 MET 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 454 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 353 GLN A 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.109375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.093505 restraints weight = 29502.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.096035 restraints weight = 20029.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097826 restraints weight = 14837.007| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8408 Z= 0.148 Angle : 0.768 20.390 11490 Z= 0.371 Chirality : 0.048 0.443 1278 Planarity : 0.005 0.044 1388 Dihedral : 5.796 54.064 1234 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.20 % Allowed : 27.38 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1016 helix: 0.68 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 470 HIS 0.003 0.001 HIS B 170 PHE 0.029 0.002 PHE A 431 TYR 0.022 0.001 TYR B 147 ARG 0.007 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 515) hydrogen bonds : angle 4.87142 ( 1521) SS BOND : bond 0.00261 ( 2) SS BOND : angle 0.52250 ( 4) covalent geometry : bond 0.00334 ( 8406) covalent geometry : angle 0.76770 (11486) *********************** 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 240 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7281 (t60) cc_final: 0.7013 (t60) REVERT: A 69 TYR cc_start: 0.7907 (t80) cc_final: 0.7706 (t80) REVERT: A 172 MET cc_start: 0.7062 (ppp) cc_final: 0.6410 (ttt) REVERT: A 287 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8277 (t70) REVERT: A 321 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.7671 (m-40) REVERT: A 322 SER cc_start: 0.8959 (m) cc_final: 0.8584 (p) REVERT: A 381 MET cc_start: 0.5525 (ttm) cc_final: 0.4738 (tmm) REVERT: A 410 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8925 (pm20) REVERT: A 454 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.8503 (t) REVERT: A 455 PHE cc_start: 0.8783 (t80) cc_final: 0.8550 (t80) REVERT: A 458 PHE cc_start: 0.9303 (m-80) cc_final: 0.8936 (m-80) REVERT: A 483 TYR cc_start: 0.6992 (t80) cc_final: 0.6641 (t80) REVERT: A 495 MET cc_start: 0.7168 (mmp) cc_final: 0.6220 (mmp) REVERT: A 522 PHE cc_start: 0.8469 (m-80) cc_final: 0.8075 (t80) REVERT: B 86 PHE cc_start: 0.8939 (m-80) cc_final: 0.8724 (m-10) REVERT: B 139 ILE cc_start: 0.9511 (tp) cc_final: 0.8756 (tp) REVERT: B 172 MET cc_start: 0.7392 (ppp) cc_final: 0.6127 (ttp) REVERT: B 228 TRP cc_start: 0.7828 (m100) cc_final: 0.7403 (m100) REVERT: B 410 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8793 (pm20) REVERT: B 446 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7507 (mpp) REVERT: B 452 MET cc_start: 0.8137 (tpp) cc_final: 0.7530 (tpp) REVERT: B 454 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.8490 (t) REVERT: B 458 PHE cc_start: 0.9209 (m-80) cc_final: 0.8947 (m-80) REVERT: B 483 TYR cc_start: 0.6260 (t80) cc_final: 0.5515 (t80) REVERT: B 495 MET cc_start: 0.7411 (mmp) cc_final: 0.6603 (mmp) REVERT: B 522 PHE cc_start: 0.8476 (m-80) cc_final: 0.8021 (t80) outliers start: 19 outliers final: 7 residues processed: 230 average time/residue: 0.1767 time to fit residues: 59.8059 Evaluate side-chains 219 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 256 MET 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 454 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.110023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.094201 restraints weight = 29839.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.096641 restraints weight = 20378.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.098529 restraints weight = 15146.827| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8408 Z= 0.147 Angle : 0.818 20.305 11490 Z= 0.388 Chirality : 0.047 0.424 1278 Planarity : 0.005 0.045 1388 Dihedral : 5.775 54.237 1234 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.32 % Allowed : 27.73 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1016 helix: 0.61 (0.19), residues: 714 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 470 HIS 0.003 0.001 HIS A 170 PHE 0.031 0.001 PHE A 431 TYR 0.032 0.002 TYR A 440 ARG 0.008 0.001 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 515) hydrogen bonds : angle 4.87383 ( 1521) SS BOND : bond 0.00215 ( 2) SS BOND : angle 0.54718 ( 4) covalent geometry : bond 0.00325 ( 8406) covalent geometry : angle 0.81771 (11486) *********************** 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 242 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.8779 (t80) cc_final: 0.8577 (t80) REVERT: A 120 PHE cc_start: 0.8296 (m-80) cc_final: 0.7969 (m-80) REVERT: A 172 MET cc_start: 0.6879 (ppp) cc_final: 0.6301 (ttt) REVERT: A 223 CYS cc_start: 0.8455 (m) cc_final: 0.8238 (p) REVERT: A 228 TRP cc_start: 0.7924 (m100) cc_final: 0.7697 (m100) REVERT: A 322 SER cc_start: 0.8888 (m) cc_final: 0.8557 (p) REVERT: A 381 MET cc_start: 0.5604 (ttm) cc_final: 0.4800 (tmm) REVERT: A 410 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: A 454 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.8503 (t) REVERT: A 458 PHE cc_start: 0.9259 (m-80) cc_final: 0.8950 (m-80) REVERT: A 483 TYR cc_start: 0.7010 (t80) cc_final: 0.6689 (t80) REVERT: A 495 MET cc_start: 0.7089 (mmp) cc_final: 0.6179 (mmp) REVERT: A 504 MET cc_start: 0.8618 (mtm) cc_final: 0.8388 (mtm) REVERT: A 522 PHE cc_start: 0.8450 (m-80) cc_final: 0.8063 (t80) REVERT: B 139 ILE cc_start: 0.9498 (tp) cc_final: 0.9094 (tp) REVERT: B 172 MET cc_start: 0.7320 (ppp) cc_final: 0.5949 (ttp) REVERT: B 327 MET cc_start: 0.8848 (ptm) cc_final: 0.8339 (ptp) REVERT: B 410 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8786 (pm20) REVERT: B 452 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7456 (tpp) REVERT: B 458 PHE cc_start: 0.9146 (m-80) cc_final: 0.8890 (m-80) REVERT: B 483 TYR cc_start: 0.6344 (t80) cc_final: 0.5563 (t80) REVERT: B 495 MET cc_start: 0.7402 (mmp) cc_final: 0.6618 (mmp) REVERT: B 522 PHE cc_start: 0.8507 (m-80) cc_final: 0.8085 (t80) outliers start: 20 outliers final: 12 residues processed: 231 average time/residue: 0.1777 time to fit residues: 60.0096 Evaluate side-chains 233 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 410 GLN 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 204 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 470 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 0.0870 chunk 36 optimal weight: 0.0040 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.111441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.095239 restraints weight = 28920.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.097734 restraints weight = 20019.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.099563 restraints weight = 14989.179| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8408 Z= 0.149 Angle : 0.832 19.777 11490 Z= 0.402 Chirality : 0.048 0.443 1278 Planarity : 0.005 0.048 1388 Dihedral : 5.791 55.499 1234 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.20 % Allowed : 28.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1016 helix: 0.56 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.49 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 228 HIS 0.003 0.001 HIS A 170 PHE 0.032 0.002 PHE A 431 TYR 0.028 0.001 TYR A 440 ARG 0.006 0.000 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 515) hydrogen bonds : angle 4.90324 ( 1521) SS BOND : bond 0.00196 ( 2) SS BOND : angle 0.51607 ( 4) covalent geometry : bond 0.00330 ( 8406) covalent geometry : angle 0.83190 (11486) ********************** 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 244 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8354 (mtp85) REVERT: A 69 TYR cc_start: 0.8061 (t80) cc_final: 0.7694 (t80) REVERT: A 71 CYS cc_start: 0.9212 (t) cc_final: 0.8969 (t) REVERT: A 96 PHE cc_start: 0.8834 (t80) cc_final: 0.8601 (t80) REVERT: A 172 MET cc_start: 0.6935 (ppp) cc_final: 0.6685 (ppp) REVERT: A 228 TRP cc_start: 0.8027 (m100) cc_final: 0.7813 (m100) REVERT: A 309 MET cc_start: 0.6740 (mmm) cc_final: 0.6370 (mmt) REVERT: A 322 SER cc_start: 0.9013 (m) cc_final: 0.8748 (p) REVERT: A 367 PRO cc_start: 0.7543 (Cg_exo) cc_final: 0.6678 (Cg_endo) REVERT: A 381 MET cc_start: 0.5371 (ttm) cc_final: 0.4642 (tmm) REVERT: A 410 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: A 454 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8492 (t) REVERT: A 458 PHE cc_start: 0.9379 (m-80) cc_final: 0.8980 (m-80) REVERT: A 483 TYR cc_start: 0.7108 (t80) cc_final: 0.6756 (t80) REVERT: A 495 MET cc_start: 0.7106 (mmp) cc_final: 0.6206 (mmp) REVERT: A 504 MET cc_start: 0.8548 (mtm) cc_final: 0.8331 (mtm) REVERT: A 522 PHE cc_start: 0.8440 (m-80) cc_final: 0.8069 (t80) REVERT: B 172 MET cc_start: 0.7434 (ppp) cc_final: 0.5987 (ttp) REVERT: B 254 PHE cc_start: 0.9134 (m-80) cc_final: 0.8810 (m-80) REVERT: B 327 MET cc_start: 0.8871 (ptm) cc_final: 0.8367 (ptp) REVERT: B 410 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8793 (pm20) REVERT: B 452 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7378 (tpp) REVERT: B 454 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.8406 (t) REVERT: B 458 PHE cc_start: 0.9221 (m-80) cc_final: 0.8900 (m-80) REVERT: B 483 TYR cc_start: 0.6327 (t80) cc_final: 0.5509 (t80) REVERT: B 495 MET cc_start: 0.7378 (mmp) cc_final: 0.6576 (mmp) REVERT: B 522 PHE cc_start: 0.8492 (m-80) cc_final: 0.8082 (t80) outliers start: 19 outliers final: 11 residues processed: 233 average time/residue: 0.1750 time to fit residues: 60.6084 Evaluate side-chains 236 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 470 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 0.0070 chunk 13 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.1980 chunk 101 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.111765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.095912 restraints weight = 29715.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.098297 restraints weight = 20727.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.100095 restraints weight = 15611.681| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8408 Z= 0.150 Angle : 0.833 18.410 11490 Z= 0.405 Chirality : 0.048 0.434 1278 Planarity : 0.005 0.048 1388 Dihedral : 5.759 56.234 1234 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.20 % Allowed : 29.23 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1016 helix: 0.58 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP B 228 HIS 0.003 0.001 HIS A 170 PHE 0.033 0.002 PHE A 431 TYR 0.024 0.001 TYR A 440 ARG 0.008 0.001 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 515) hydrogen bonds : angle 4.95531 ( 1521) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.48124 ( 4) covalent geometry : bond 0.00329 ( 8406) covalent geometry : angle 0.83299 (11486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3681.64 seconds wall clock time: 68 minutes 54.70 seconds (4134.70 seconds total)