Starting phenix.real_space_refine on Fri Oct 23 15:10:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28lw_56604/10_2026/28lw_56604.cif Found real_map, /net/cci-nas-00/data/ceres_data/28lw_56604/10_2026/28lw_56604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28lw_56604/10_2026/28lw_56604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28lw_56604/10_2026/28lw_56604.map" model { file = "/net/cci-nas-00/data/ceres_data/28lw_56604/10_2026/28lw_56604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28lw_56604/10_2026/28lw_56604.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 80 5.16 5 C 6422 2.51 5 N 1731 2.21 5 O 1885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10130 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5057 Classifications: {'peptide': 660} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 631} Chain breaks: 1 Chain: "B" Number of atoms: 5049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5049 Classifications: {'peptide': 659} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 630} Chain breaks: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 717 SG CYS A 137 62.553 48.495 46.939 1.00 98.04 S ATOM 684 SG CYS A 132 57.188 45.777 45.196 1.00 94.68 S ATOM 795 SG CYS A 148 57.366 51.927 45.500 1.00101.56 S ATOM 661 SG CYS A 129 57.934 48.760 51.210 1.00 99.84 S ATOM 655 SG CYS A 128 63.424 45.874 54.725 1.00 93.62 S ATOM 602 SG CYS A 120 68.167 45.550 59.000 1.00109.84 S ATOM 5651 SG CYS B 120 68.456 42.239 53.860 1.00109.42 S ATOM 5704 SG CYS B 128 63.300 41.034 58.030 1.00100.00 S ATOM 5710 SG CYS B 129 58.425 37.704 61.762 1.00 93.87 S ATOM 5733 SG CYS B 132 57.317 40.764 67.707 1.00 96.20 S ATOM 5766 SG CYS B 137 62.905 38.257 65.855 1.00 97.59 S ATOM 5844 SG CYS B 148 57.839 34.546 67.343 1.00100.36 S Time building chain proxies: 2.12, per 1000 atoms: 0.21 Number of scatterers: 10130 At special positions: 0 Unit cell: (86.45, 85.15, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 80 16.00 O 1885 8.00 N 1731 7.00 C 6422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 398.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 801 " pdb="FE2 SF4 A 801 " - pdb=" SG CYS A 132 " pdb="FE3 SF4 A 801 " - pdb=" SG CYS A 148 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 137 " pdb="FE4 SF4 A 801 " - pdb=" SG CYS A 129 " pdb=" SF4 B 801 " pdb="FE1 SF4 B 801 " - pdb=" SG CYS A 128 " pdb="FE3 SF4 B 801 " - pdb=" SG CYS B 120 " pdb="FE4 SF4 B 801 " - pdb=" SG CYS B 128 " pdb="FE2 SF4 B 801 " - pdb=" SG CYS A 120 " pdb=" SF4 B 802 " pdb="FE2 SF4 B 802 " - pdb=" SG CYS B 132 " pdb="FE4 SF4 B 802 " - pdb=" SG CYS B 148 " pdb="FE3 SF4 B 802 " - pdb=" SG CYS B 137 " pdb="FE1 SF4 B 802 " - pdb=" SG CYS B 129 " Number of angles added : 36 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2414 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 60.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 61 through 77 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 105 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 151 through 188 removed outlier: 3.722A pdb=" N HIS A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.503A pdb=" N GLU A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 282 through 301 Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 341 through 353 removed outlier: 4.062A pdb=" N VAL A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.683A pdb=" N LEU A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 404 removed outlier: 3.840A pdb=" N GLY A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.962A pdb=" N CYS A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 476 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 506 through 515 Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 569 through 576 removed outlier: 3.773A pdb=" N LYS A 573 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 599 through 614 Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 660 through 669 Processing helix chain 'A' and resid 670 through 675 removed outlier: 3.947A pdb=" N THR A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 704 Processing helix chain 'B' and resid 62 through 77 removed outlier: 3.684A pdb=" N LYS B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 105 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 151 through 188 removed outlier: 3.879A pdb=" N HIS B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 215 through 233 Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.522A pdb=" N SER B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.620A pdb=" N ALA B 327 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 4.228A pdb=" N VAL B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.770A pdb=" N LEU B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.843A pdb=" N VAL B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.528A pdb=" N GLU B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 515 Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'B' and resid 558 through 565 removed outlier: 4.345A pdb=" N LEU B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 577 through 585 Processing helix chain 'B' and resid 596 through 598 No H-bonds generated for 'chain 'B' and resid 596 through 598' Processing helix chain 'B' and resid 599 through 615 Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.545A pdb=" N ALA B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 Processing helix chain 'B' and resid 670 through 675 removed outlier: 3.913A pdb=" N THR B 674 " --> pdb=" O GLY B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 704 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 323 Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 392 removed outlier: 9.416A pdb=" N ILE A 389 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE A 371 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU A 391 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL A 333 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TYR A 372 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 335 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 374 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL A 337 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER A 435 " --> pdb=" O TYR A 446 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR A 448 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 595 removed outlier: 6.597A pdb=" N ILE A 552 " --> pdb=" O TRP A 592 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A 594 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N SER A 554 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL A 522 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASN A 555 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET A 524 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N TYR A 650 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 625 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA8, first strand: chain 'B' and resid 319 through 323 Processing sheet with id=AA9, first strand: chain 'B' and resid 388 through 392 removed outlier: 9.556A pdb=" N ILE B 389 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE B 371 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU B 391 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLY B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 333 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR B 372 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE B 335 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE B 374 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 337 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN B 334 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 410 " --> pdb=" O ASN B 334 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 336 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP B 409 " --> pdb=" O VAL B 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 591 through 595 removed outlier: 8.308A pdb=" N TRP B 592 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 552 " --> pdb=" O TRP B 592 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 594 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N SER B 554 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY B 520 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE B 553 " --> pdb=" O GLY B 520 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL B 522 " --> pdb=" O ILE B 553 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN B 555 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET B 524 " --> pdb=" O ASN B 555 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N TYR B 650 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE B 625 " --> pdb=" O TYR B 650 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 4276 1.43 - 1.65: 5930 1.65 - 1.86: 100 1.86 - 2.07: 0 2.07 - 2.28: 36 Bond restraints: 10342 Sorted by residual: bond pdb=" N ILE A 36 " pdb=" CA ILE A 36 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N ILE B 36 " pdb=" CA ILE B 36 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" CG1 ILE A 400 " pdb=" CD1 ILE A 400 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.58e+00 bond pdb=" CG1 ILE B 400 " pdb=" CD1 ILE B 400 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.88e-01 bond pdb=" CG ARG B 476 " pdb=" CD ARG B 476 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.80e-01 ... (remaining 10337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 13294 1.04 - 2.09: 571 2.09 - 3.13: 90 3.13 - 4.17: 41 4.17 - 5.22: 8 Bond angle restraints: 14004 Sorted by residual: angle pdb=" CA TYR A 68 " pdb=" CB TYR A 68 " pdb=" CG TYR A 68 " ideal model delta sigma weight residual 113.90 119.12 -5.22 1.80e+00 3.09e-01 8.40e+00 angle pdb=" CA TYR B 68 " pdb=" CB TYR B 68 " pdb=" CG TYR B 68 " ideal model delta sigma weight residual 113.90 118.57 -4.67 1.80e+00 3.09e-01 6.74e+00 angle pdb=" N TYR A 446 " pdb=" CA TYR A 446 " pdb=" C TYR A 446 " ideal model delta sigma weight residual 110.44 107.53 2.91 1.20e+00 6.94e-01 5.89e+00 angle pdb=" N VAL A 413 " pdb=" CA VAL A 413 " pdb=" C VAL A 413 " ideal model delta sigma weight residual 109.34 114.22 -4.88 2.08e+00 2.31e-01 5.50e+00 angle pdb=" N GLY A 504 " pdb=" CA GLY A 504 " pdb=" C GLY A 504 " ideal model delta sigma weight residual 114.67 111.41 3.26 1.41e+00 5.03e-01 5.35e+00 ... (remaining 13999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 5428 18.04 - 36.07: 555 36.07 - 54.11: 177 54.11 - 72.14: 36 72.14 - 90.18: 17 Dihedral angle restraints: 6213 sinusoidal: 2444 harmonic: 3769 Sorted by residual: dihedral pdb=" CA TYR B 446 " pdb=" C TYR B 446 " pdb=" N GLU B 447 " pdb=" CA GLU B 447 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASP A 599 " pdb=" C ASP A 599 " pdb=" N ASN A 600 " pdb=" CA ASN A 600 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA VAL A 413 " pdb=" C VAL A 413 " pdb=" N GLN A 414 " pdb=" CA GLN A 414 " ideal model delta harmonic sigma weight residual 180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 6210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 902 0.028 - 0.056: 404 0.056 - 0.084: 138 0.084 - 0.112: 87 0.112 - 0.140: 38 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CA ILE A 553 " pdb=" N ILE A 553 " pdb=" C ILE A 553 " pdb=" CB ILE A 553 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE B 479 " pdb=" N ILE B 479 " pdb=" C ILE B 479 " pdb=" CB ILE B 479 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE B 518 " pdb=" N ILE B 518 " pdb=" C ILE B 518 " pdb=" CB ILE B 518 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1566 not shown) Planarity restraints: 1801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 89 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO B 90 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 529 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO B 530 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 530 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 530 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 483 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO B 484 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 484 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 484 " 0.024 5.00e-02 4.00e+02 ... (remaining 1798 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3777 2.88 - 3.39: 10511 3.39 - 3.89: 17938 3.89 - 4.40: 21894 4.40 - 4.90: 36084 Nonbonded interactions: 90204 Sorted by model distance: nonbonded pdb=" O GLU B 177 " pdb=" OE1 GLU B 177 " model vdw 2.380 3.040 nonbonded pdb=" O ARG B 162 " pdb=" OH TYR B 272 " model vdw 2.397 3.040 nonbonded pdb=" O LYS A 507 " pdb=" OE1 GLU A 511 " model vdw 2.412 3.040 nonbonded pdb=" OG SER B 396 " pdb=" OH TYR B 534 " model vdw 2.420 3.040 nonbonded pdb=" O GLN B 252 " pdb=" OD1 ASP B 256 " model vdw 2.425 3.040 ... (remaining 90199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 36 through 48 or resid 61 through 801)) selection = (chain 'B' and resid 36 through 801) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.580 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.004 0.063 10354 Z= 0.179 Angle : 0.622 16.461 14040 Z= 0.291 Chirality : 0.043 0.140 1569 Planarity : 0.005 0.059 1801 Dihedral : 16.977 90.180 3799 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer: Outliers : 1.86 % Allowed : 17.99 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1311 helix: 1.12 (0.19), residues: 735 sheet: -1.04 (0.48), residues: 102 loop : -0.59 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 439 TYR 0.025 0.002 TYR A 498 PHE 0.020 0.002 PHE B 290 TRP 0.008 0.001 TRP B 409 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (10342) covalent geometry : angle 0.52868 / 0.29 (14004) hydrogen bonds : bond 0.13513 / 9.15 ( 559) hydrogen bonds : angle 6.70217 / 4.72 ( 1620) metal coordination : bond 0.01497 / 0.79 ( 12) metal coordination : angle 6.47546 / 3.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7000 (t0) cc_final: 0.6043 (m-30) REVERT: A 102 GLU cc_start: 0.8750 (tt0) cc_final: 0.8491 (tt0) REVERT: A 199 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7458 (tttp) REVERT: A 369 ILE cc_start: 0.8420 (mt) cc_final: 0.8218 (mp) REVERT: A 385 TYR cc_start: 0.7621 (p90) cc_final: 0.7325 (p90) REVERT: A 665 GLU cc_start: 0.8479 (tt0) cc_final: 0.7889 (tm-30) REVERT: A 683 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 691 LYS cc_start: 0.8956 (tttm) cc_final: 0.8469 (ttmm) REVERT: A 695 ASP cc_start: 0.7991 (m-30) cc_final: 0.7779 (m-30) REVERT: B 67 ASP cc_start: 0.8165 (m-30) cc_final: 0.7872 (m-30) REVERT: B 138 ARG cc_start: 0.8194 (ptt180) cc_final: 0.7658 (ptp-170) REVERT: B 284 LYS cc_start: 0.7668 (mttm) cc_final: 0.7458 (mmpt) REVERT: B 359 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8237 (pp20) REVERT: B 433 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8332 (t) REVERT: B 482 TYR cc_start: 0.7936 (t80) cc_final: 0.6962 (t80) REVERT: B 540 ASP cc_start: 0.8321 (m-30) cc_final: 0.8101 (t0) REVERT: B 547 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8601 (mmtm) outliers start: 20 outliers final: 6 residues processed: 231 average time/residue: 0.5567 time to fit residues: 137.8626 Evaluate side-chains 121 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 683 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.089773 restraints weight = 18205.744| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.57 r_work: 0.3399 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10354 Z= 0.147 Angle : 0.666 16.085 14040 Z= 0.315 Chirality : 0.045 0.155 1569 Planarity : 0.004 0.042 1801 Dihedral : 5.560 52.085 1427 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.10 % Rotamer: Outliers : 4.66 % Allowed : 19.57 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.23), residues: 1311 helix: 1.55 (0.19), residues: 750 sheet: -0.78 (0.47), residues: 106 loop : -0.38 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 354 TYR 0.027 0.002 TYR A 272 PHE 0.018 0.002 PHE B 290 TRP 0.014 0.001 TRP B 184 HIS 0.008 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10342) covalent geometry : angle 0.58395 / 0.31 (14004) hydrogen bonds : bond 0.04205 / 2.79 ( 559) hydrogen bonds : angle 4.97985 / 3.47 ( 1620) metal coordination : bond 0.01015 / 0.55 ( 12) metal coordination : angle 6.36041 / 3.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8067 (tptp) REVERT: A 213 ASN cc_start: 0.7876 (p0) cc_final: 0.7649 (p0) REVERT: A 229 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: A 367 LYS cc_start: 0.8656 (mptt) cc_final: 0.8439 (mptt) REVERT: A 385 TYR cc_start: 0.7735 (p90) cc_final: 0.7375 (p90) REVERT: A 428 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8258 (mptt) REVERT: A 518 ILE cc_start: 0.7469 (mm) cc_final: 0.7193 (mm) REVERT: A 665 GLU cc_start: 0.8509 (tt0) cc_final: 0.7996 (tm-30) REVERT: A 683 THR cc_start: 0.8787 (m) cc_final: 0.8473 (p) REVERT: B 67 ASP cc_start: 0.8266 (m-30) cc_final: 0.8003 (m-30) REVERT: B 73 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (p) REVERT: B 138 ARG cc_start: 0.8222 (ptt180) cc_final: 0.7648 (ptp-170) REVERT: B 211 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: B 284 LYS cc_start: 0.7712 (mttm) cc_final: 0.7493 (mmpt) REVERT: B 359 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8210 (pp20) REVERT: B 482 TYR cc_start: 0.8081 (t80) cc_final: 0.7205 (t80) REVERT: B 540 ASP cc_start: 0.8460 (m-30) cc_final: 0.8208 (m-30) REVERT: B 547 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8416 (tttp) REVERT: B 701 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8255 (mmmt) outliers start: 50 outliers final: 14 residues processed: 160 average time/residue: 0.5099 time to fit residues: 88.4571 Evaluate side-chains 119 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [126, 9, 117, 110, 68, 94, 49, 1, 95, 63, 29] chunk 126 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN B 174 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.096009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081506 restraints weight = 19131.182| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.55 r_work: 0.3207 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10354 Z= 0.271 Angle : 0.772 25.153 14040 Z= 0.349 Chirality : 0.048 0.168 1569 Planarity : 0.005 0.046 1801 Dihedral : 5.244 55.790 1419 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 4.85 % Allowed : 18.92 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1311 helix: 1.38 (0.19), residues: 745 sheet: -0.43 (0.51), residues: 104 loop : -0.25 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 439 TYR 0.023 0.002 TYR A 68 PHE 0.023 0.002 PHE B 290 TRP 0.009 0.002 TRP A 630 HIS 0.007 0.002 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 (10342) covalent geometry : angle 0.64897 / 0.35 (14004) hydrogen bonds : bond 0.05150 / 3.38 ( 559) hydrogen bonds : angle 5.03616 / 3.53 ( 1620) metal coordination : bond 0.02406 / 1.30 ( 12) metal coordination : angle 8.27526 / 4.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 95 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8425 (m) REVERT: A 367 LYS cc_start: 0.8553 (mptt) cc_final: 0.8184 (mptt) REVERT: A 385 TYR cc_start: 0.8059 (p90) cc_final: 0.7782 (p90) REVERT: A 428 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8233 (mptt) REVERT: A 665 GLU cc_start: 0.8585 (tt0) cc_final: 0.7992 (tm-30) REVERT: A 695 ASP cc_start: 0.8161 (m-30) cc_final: 0.7951 (m-30) REVERT: B 73 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8618 (p) REVERT: B 214 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7703 (ttp80) REVERT: B 284 LYS cc_start: 0.7857 (mttm) cc_final: 0.7642 (mmpt) REVERT: B 300 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.8949 (m) REVERT: B 359 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8176 (pp20) REVERT: B 482 TYR cc_start: 0.8102 (t80) cc_final: 0.7341 (t80) REVERT: B 533 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6482 (tt) REVERT: B 540 ASP cc_start: 0.8602 (m-30) cc_final: 0.8308 (m-30) REVERT: B 547 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8519 (tttp) outliers start: 52 outliers final: 20 residues processed: 132 average time/residue: 0.5213 time to fit residues: 74.3083 Evaluate side-chains 114 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [99, 39, 92, 13, 68, 16, 90, 113, 18, 116, 60] chunk 99 optimal weight: 0.2980 chunk 39 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN B 174 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.086846 restraints weight = 18637.047| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.57 r_work: 0.3354 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10354 Z= 0.108 Angle : 0.630 16.537 14040 Z= 0.280 Chirality : 0.043 0.150 1569 Planarity : 0.004 0.046 1801 Dihedral : 5.069 56.568 1419 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.17 % Allowed : 21.90 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.23), residues: 1311 helix: 1.71 (0.19), residues: 744 sheet: -0.18 (0.49), residues: 116 loop : -0.20 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.018 0.001 TYR A 68 PHE 0.016 0.001 PHE B 290 TRP 0.009 0.001 TRP A 184 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (10342) covalent geometry : angle 0.52518 / 0.28 (14004) hydrogen bonds : bond 0.03647 / 2.40 ( 559) hydrogen bonds : angle 4.64160 / 3.23 ( 1620) metal coordination : bond 0.00655 / 0.34 ( 12) metal coordination : angle 6.87834 / 4.12 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8215 (t0) cc_final: 0.7947 (t0) REVERT: A 367 LYS cc_start: 0.8601 (mptt) cc_final: 0.8238 (mptt) REVERT: A 385 TYR cc_start: 0.8012 (p90) cc_final: 0.7690 (p90) REVERT: A 428 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8239 (mptt) REVERT: A 471 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 511 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: A 665 GLU cc_start: 0.8515 (tt0) cc_final: 0.7964 (tm-30) REVERT: A 695 ASP cc_start: 0.8151 (m-30) cc_final: 0.7926 (m-30) REVERT: B 67 ASP cc_start: 0.8227 (m-30) cc_final: 0.7841 (m-30) REVERT: B 73 SER cc_start: 0.8812 (t) cc_final: 0.8605 (p) REVERT: B 284 LYS cc_start: 0.7903 (mttm) cc_final: 0.7643 (mmpt) REVERT: B 300 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8427 (m) REVERT: B 315 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 359 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8195 (pp20) REVERT: B 482 TYR cc_start: 0.7968 (t80) cc_final: 0.7361 (t80) REVERT: B 540 ASP cc_start: 0.8534 (m-30) cc_final: 0.8257 (m-30) REVERT: B 547 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8571 (tttm) REVERT: B 554 SER cc_start: 0.8958 (t) cc_final: 0.8745 (t) outliers start: 34 outliers final: 17 residues processed: 140 average time/residue: 0.5220 time to fit residues: 78.9270 Evaluate side-chains 115 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 603 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [10, 107, 122, 43, 52, 2, 66, 48, 29, 88, 25] chunk 10 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 43 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084853 restraints weight = 18884.768| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.48 r_work: 0.3255 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10354 Z= 0.229 Angle : 0.709 22.232 14040 Z= 0.320 Chirality : 0.046 0.167 1569 Planarity : 0.004 0.047 1801 Dihedral : 5.049 57.644 1419 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 4.01 % Allowed : 21.99 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1311 helix: 1.65 (0.19), residues: 744 sheet: 0.02 (0.50), residues: 114 loop : -0.21 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 354 TYR 0.023 0.002 TYR A 68 PHE 0.022 0.002 PHE B 290 TRP 0.006 0.001 TRP A 630 HIS 0.010 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (10342) covalent geometry : angle 0.59951 / 0.32 (14004) hydrogen bonds : bond 0.04484 / 2.96 ( 559) hydrogen bonds : angle 4.76460 / 3.33 ( 1620) metal coordination : bond 0.01995 / 1.09 ( 12) metal coordination : angle 7.51287 / 4.43 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8209 (t0) cc_final: 0.7924 (t0) REVERT: A 212 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8460 (tmmt) REVERT: A 367 LYS cc_start: 0.8602 (mptt) cc_final: 0.8234 (mptt) REVERT: A 428 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8272 (mptt) REVERT: A 471 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 665 GLU cc_start: 0.8422 (tt0) cc_final: 0.7894 (tm-30) REVERT: B 73 SER cc_start: 0.8852 (t) cc_final: 0.8635 (p) REVERT: B 284 LYS cc_start: 0.7948 (mttm) cc_final: 0.7717 (mmpt) REVERT: B 300 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8780 (m) REVERT: B 359 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8237 (pp20) REVERT: B 482 TYR cc_start: 0.7988 (t80) cc_final: 0.7369 (t80) REVERT: B 540 ASP cc_start: 0.8585 (m-30) cc_final: 0.8290 (m-30) REVERT: B 547 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8600 (tttm) outliers start: 43 outliers final: 24 residues processed: 131 average time/residue: 0.5181 time to fit residues: 73.3099 Evaluate side-chains 115 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 626 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [44, 17, 20, 100, 121, 95, 76, 18, 96, 65, 52] chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084876 restraints weight = 18774.835| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.56 r_work: 0.3324 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10354 Z= 0.130 Angle : 0.653 18.914 14040 Z= 0.290 Chirality : 0.043 0.157 1569 Planarity : 0.004 0.048 1801 Dihedral : 5.006 58.245 1419 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 3.17 % Allowed : 23.02 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.23), residues: 1311 helix: 1.75 (0.19), residues: 744 sheet: 0.16 (0.50), residues: 114 loop : -0.16 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 439 TYR 0.019 0.001 TYR A 68 PHE 0.018 0.002 PHE B 290 TRP 0.008 0.001 TRP A 630 HIS 0.008 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10342) covalent geometry : angle 0.54778 / 0.29 (14004) hydrogen bonds : bond 0.03840 / 2.53 ( 559) hydrogen bonds : angle 4.61266 / 3.21 ( 1620) metal coordination : bond 0.01086 / 0.57 ( 12) metal coordination : angle 7.05315 / 4.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8224 (t0) cc_final: 0.7937 (t0) REVERT: A 212 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8463 (tmmt) REVERT: A 238 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: A 367 LYS cc_start: 0.8567 (mptt) cc_final: 0.8171 (mptt) REVERT: A 428 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8246 (mptt) REVERT: A 471 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 533 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7126 (tm) REVERT: A 665 GLU cc_start: 0.8448 (tt0) cc_final: 0.7911 (tm-30) REVERT: B 73 SER cc_start: 0.8821 (t) cc_final: 0.8611 (p) REVERT: B 284 LYS cc_start: 0.7946 (mttm) cc_final: 0.7704 (mmpt) REVERT: B 300 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 359 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8210 (pp20) REVERT: B 482 TYR cc_start: 0.7917 (t80) cc_final: 0.7424 (t80) REVERT: B 540 ASP cc_start: 0.8550 (m-30) cc_final: 0.8255 (m-30) REVERT: B 547 LYS cc_start: 0.8824 (mmtm) cc_final: 0.8616 (tttm) REVERT: B 554 SER cc_start: 0.8976 (t) cc_final: 0.8775 (t) outliers start: 34 outliers final: 18 residues processed: 131 average time/residue: 0.5100 time to fit residues: 72.4101 Evaluate side-chains 117 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [60, 37, 80, 13, 18, 124, 98, 30, 130, 122, 72] chunk 60 optimal weight: 0.0470 chunk 37 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086535 restraints weight = 18693.547| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.48 r_work: 0.3283 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10354 Z= 0.161 Angle : 0.675 20.231 14040 Z= 0.302 Chirality : 0.044 0.160 1569 Planarity : 0.004 0.047 1801 Dihedral : 4.989 58.862 1419 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 2.52 % Allowed : 23.67 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.23), residues: 1311 helix: 1.74 (0.19), residues: 744 sheet: 0.23 (0.51), residues: 114 loop : -0.14 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 439 TYR 0.021 0.001 TYR A 68 PHE 0.019 0.002 PHE B 290 TRP 0.013 0.001 TRP B 184 HIS 0.007 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10342) covalent geometry : angle 0.57143 / 0.30 (14004) hydrogen bonds : bond 0.03971 / 2.61 ( 559) hydrogen bonds : angle 4.62330 / 3.22 ( 1620) metal coordination : bond 0.01395 / 0.74 ( 12) metal coordination : angle 7.10299 / 4.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8197 (t0) cc_final: 0.7900 (t0) REVERT: A 212 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8506 (tmmt) REVERT: A 367 LYS cc_start: 0.8563 (mptt) cc_final: 0.8158 (mptt) REVERT: A 428 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8259 (mptt) REVERT: A 471 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 533 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7210 (tm) REVERT: A 656 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: A 665 GLU cc_start: 0.8427 (tt0) cc_final: 0.7897 (tm-30) REVERT: B 73 SER cc_start: 0.8818 (t) cc_final: 0.8614 (p) REVERT: B 284 LYS cc_start: 0.7956 (mttm) cc_final: 0.7716 (mmpt) REVERT: B 300 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8603 (m) REVERT: B 359 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8228 (pp20) REVERT: B 482 TYR cc_start: 0.7917 (t80) cc_final: 0.7493 (t80) REVERT: B 540 ASP cc_start: 0.8568 (m-30) cc_final: 0.8278 (m-30) REVERT: B 547 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8634 (tttm) outliers start: 27 outliers final: 19 residues processed: 118 average time/residue: 0.5315 time to fit residues: 67.7443 Evaluate side-chains 111 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 626 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [43, 120, 58, 25, 118, 119, 77, 111, 12, 6, 31] chunk 43 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.100932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086928 restraints weight = 18700.474| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.46 r_work: 0.3296 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10354 Z= 0.146 Angle : 0.667 19.978 14040 Z= 0.297 Chirality : 0.044 0.160 1569 Planarity : 0.004 0.047 1801 Dihedral : 4.990 59.358 1419 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.05 % Allowed : 24.04 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.23), residues: 1311 helix: 1.77 (0.19), residues: 745 sheet: 0.21 (0.54), residues: 104 loop : -0.14 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 354 TYR 0.021 0.001 TYR A 68 PHE 0.019 0.002 PHE B 290 TRP 0.009 0.001 TRP B 184 HIS 0.007 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10342) covalent geometry : angle 0.56457 / 0.30 (14004) hydrogen bonds : bond 0.03877 / 2.55 ( 559) hydrogen bonds : angle 4.58954 / 3.19 ( 1620) metal coordination : bond 0.01256 / 0.66 ( 12) metal coordination : angle 7.02384 / 4.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8187 (t0) cc_final: 0.7891 (t0) REVERT: A 238 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: A 367 LYS cc_start: 0.8576 (mptt) cc_final: 0.8174 (mptt) REVERT: A 428 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8269 (mptt) REVERT: A 471 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8204 (tm-30) REVERT: A 533 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7218 (tm) REVERT: A 665 GLU cc_start: 0.8425 (tt0) cc_final: 0.7890 (tm-30) REVERT: B 300 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8578 (m) REVERT: B 359 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8239 (pp20) REVERT: B 482 TYR cc_start: 0.7897 (t80) cc_final: 0.7484 (t80) REVERT: B 540 ASP cc_start: 0.8565 (m-30) cc_final: 0.8265 (m-30) outliers start: 22 outliers final: 16 residues processed: 112 average time/residue: 0.5167 time to fit residues: 62.6364 Evaluate side-chains 106 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [116, 56, 96, 78, 40, 84, 47, 22, 46, 24, 43] chunk 116 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.087149 restraints weight = 18700.754| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.50 r_work: 0.3298 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10354 Z= 0.143 Angle : 0.668 19.488 14040 Z= 0.301 Chirality : 0.044 0.163 1569 Planarity : 0.004 0.047 1801 Dihedral : 4.977 59.947 1419 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.42 % Allowed : 24.23 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1311 helix: 1.81 (0.19), residues: 745 sheet: 0.16 (0.50), residues: 116 loop : -0.07 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 354 TYR 0.021 0.001 TYR B 68 PHE 0.019 0.002 PHE B 290 TRP 0.008 0.001 TRP B 184 HIS 0.007 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10342) covalent geometry : angle 0.57078 / 0.30 (14004) hydrogen bonds : bond 0.03814 / 2.51 ( 559) hydrogen bonds : angle 4.55029 / 3.17 ( 1620) metal coordination : bond 0.01184 / 0.61 ( 12) metal coordination : angle 6.86415 / 4.13 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8137 (t0) cc_final: 0.7834 (t0) REVERT: A 238 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: A 367 LYS cc_start: 0.8580 (mptt) cc_final: 0.8189 (mptt) REVERT: A 428 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8234 (mptt) REVERT: A 471 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 533 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7142 (tm) REVERT: A 621 MET cc_start: 0.7890 (mmm) cc_final: 0.6265 (mpt) REVERT: A 656 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: A 665 GLU cc_start: 0.8401 (tt0) cc_final: 0.7847 (tm-30) REVERT: B 74 GLU cc_start: 0.8049 (pt0) cc_final: 0.7844 (pm20) REVERT: B 300 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8533 (m) REVERT: B 359 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8253 (pp20) REVERT: B 482 TYR cc_start: 0.7949 (t80) cc_final: 0.7518 (t80) REVERT: B 540 ASP cc_start: 0.8553 (m-30) cc_final: 0.8250 (m-30) outliers start: 26 outliers final: 17 residues processed: 110 average time/residue: 0.5056 time to fit residues: 60.3734 Evaluate side-chains 107 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 626 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [97, 21, 123, 63, 85, 0, 91, 104, 49, 105, 73] chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.101367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.087251 restraints weight = 18491.611| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.49 r_work: 0.3337 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10354 Z= 0.139 Angle : 0.663 19.265 14040 Z= 0.297 Chirality : 0.044 0.179 1569 Planarity : 0.004 0.047 1801 Dihedral : 4.969 59.401 1419 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.24 % Allowed : 24.42 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.23), residues: 1311 helix: 1.83 (0.19), residues: 745 sheet: 0.28 (0.50), residues: 114 loop : -0.07 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 354 TYR 0.020 0.001 TYR B 68 PHE 0.019 0.002 PHE B 290 TRP 0.010 0.001 TRP B 184 HIS 0.007 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10342) covalent geometry : angle 0.56606 / 0.30 (14004) hydrogen bonds : bond 0.03773 / 2.48 ( 559) hydrogen bonds : angle 4.53290 / 3.15 ( 1620) metal coordination : bond 0.01143 / 0.59 ( 12) metal coordination : angle 6.82292 / 4.11 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8133 (t0) cc_final: 0.7834 (t0) REVERT: A 238 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: A 367 LYS cc_start: 0.8580 (mptt) cc_final: 0.8187 (mptt) REVERT: A 428 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8229 (mptt) REVERT: A 471 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 533 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7145 (tm) REVERT: A 621 MET cc_start: 0.7879 (mmm) cc_final: 0.6354 (mpt) REVERT: A 656 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: A 665 GLU cc_start: 0.8386 (tt0) cc_final: 0.7826 (tm-30) REVERT: B 74 GLU cc_start: 0.8026 (pt0) cc_final: 0.7821 (pm20) REVERT: B 300 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8514 (m) REVERT: B 359 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8267 (pp20) REVERT: B 482 TYR cc_start: 0.7940 (t80) cc_final: 0.7507 (t80) REVERT: B 540 ASP cc_start: 0.8560 (m-30) cc_final: 0.8256 (m-30) outliers start: 24 outliers final: 17 residues processed: 109 average time/residue: 0.5070 time to fit residues: 59.9238 Evaluate side-chains 108 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 626 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [123, 36, 57, 35, 89, 28, 67, 32, 56, 85, 117] chunk 123 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.0170 chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088526 restraints weight = 18489.176| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.55 r_work: 0.3318 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10354 Z= 0.117 Angle : 0.655 16.702 14040 Z= 0.296 Chirality : 0.043 0.160 1569 Planarity : 0.004 0.047 1801 Dihedral : 4.926 58.403 1419 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.86 % Allowed : 24.98 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.23), residues: 1311 helix: 1.90 (0.19), residues: 744 sheet: 0.28 (0.48), residues: 124 loop : -0.05 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 354 TYR 0.019 0.001 TYR B 68 PHE 0.017 0.001 PHE B 290 TRP 0.011 0.001 TRP B 184 HIS 0.008 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10342) covalent geometry : angle 0.56687 / 0.30 (14004) hydrogen bonds : bond 0.03481 / 2.29 ( 559) hydrogen bonds : angle 4.45692 / 3.10 ( 1620) metal coordination : bond 0.00746 / 0.38 ( 12) metal coordination : angle 6.50038 / 3.94 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3121.82 seconds wall clock time: 54 minutes 13.67 seconds (3253.67 seconds total)