Starting phenix.real_space_refine on Wed Jun 11 08:22:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wjm_32545/06_2025/7wjm_32545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wjm_32545/06_2025/7wjm_32545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wjm_32545/06_2025/7wjm_32545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wjm_32545/06_2025/7wjm_32545.map" model { file = "/net/cci-nas-00/data/ceres_data/7wjm_32545/06_2025/7wjm_32545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wjm_32545/06_2025/7wjm_32545.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8426 2.51 5 N 2160 2.21 5 O 2312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12970 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6485 Classifications: {'peptide': 807} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 774} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 13.89, per 1000 atoms: 1.07 Number of scatterers: 12970 At special positions: 0 Unit cell: (120.91, 116.63, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2312 8.00 N 2160 7.00 C 8426 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: 3.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 65.6% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.703A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 112 through 131 removed outlier: 3.830A pdb=" N ALA A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.942A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.615A pdb=" N HIS A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 448 removed outlier: 3.642A pdb=" N SER A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.708A pdb=" N LEU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 removed outlier: 3.658A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 505 removed outlier: 3.802A pdb=" N LEU A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 554 removed outlier: 3.856A pdb=" N LEU A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.748A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 619 through 647 removed outlier: 3.992A pdb=" N ASP A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 681 Processing helix chain 'A' and resid 684 through 705 removed outlier: 5.245A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 5.105A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 720 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 Processing helix chain 'A' and resid 764 through 819 Processing helix chain 'A' and resid 824 through 857 removed outlier: 4.855A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 77 through 91 removed outlier: 3.701A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 112 through 131 removed outlier: 3.830A pdb=" N ALA B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 162 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.942A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 357 through 374 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.616A pdb=" N HIS B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 448 removed outlier: 3.642A pdb=" N SER B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.709A pdb=" N LEU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.658A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 removed outlier: 3.803A pdb=" N LEU B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 554 removed outlier: 3.856A pdb=" N LEU B 532 " --> pdb=" O ASP B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 587 removed outlier: 3.748A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 606 Processing helix chain 'B' and resid 619 through 647 removed outlier: 3.992A pdb=" N ASP B 623 " --> pdb=" O GLN B 619 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 681 Processing helix chain 'B' and resid 684 through 705 removed outlier: 5.244A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.106A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 720 " --> pdb=" O THR B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 Processing helix chain 'B' and resid 764 through 819 Processing helix chain 'B' and resid 824 through 857 removed outlier: 4.855A pdb=" N GLY B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 6.293A pdb=" N HIS B 175 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 326 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N HIS B 514 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 408 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 516 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY B 410 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASP B 518 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N LEU B 412 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL B 520 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N VAL B 414 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG B 522 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 387 removed outlier: 7.546A pdb=" N HIS A 514 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA A 408 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A 516 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY A 410 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP A 518 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N LEU A 412 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL A 520 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N VAL A 414 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG A 522 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 326 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N HIS A 175 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 174 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER B 55 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 176 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337 834 hydrogen bonds defined for protein. 2460 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: 4.31 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4100 1.34 - 1.46: 2750 1.46 - 1.57: 6362 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 13324 Sorted by residual: bond pdb=" C SER B 534 " pdb=" O SER B 534 " ideal model delta sigma weight residual 1.237 1.248 -0.012 1.16e-02 7.43e+03 1.03e+00 bond pdb=" C SER A 534 " pdb=" O SER A 534 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.16e-02 7.43e+03 9.53e-01 bond pdb=" C ASN A 541 " pdb=" O ASN A 541 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 9.10e-01 bond pdb=" C ASN B 541 " pdb=" O ASN B 541 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.50e-01 bond pdb=" C PRO A 649 " pdb=" N LYS A 650 " ideal model delta sigma weight residual 1.332 1.320 0.013 1.40e-02 5.10e+03 8.06e-01 ... (remaining 13319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 17572 1.13 - 2.26: 387 2.26 - 3.39: 95 3.39 - 4.52: 28 4.52 - 5.65: 12 Bond angle restraints: 18094 Sorted by residual: angle pdb=" C GLY B 277 " pdb=" N ASP B 278 " pdb=" CA ASP B 278 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.74e+00 angle pdb=" C GLY A 277 " pdb=" N ASP A 278 " pdb=" CA ASP A 278 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.52e+00 angle pdb=" C PHE B 601 " pdb=" N GLN B 602 " pdb=" CA GLN B 602 " ideal model delta sigma weight residual 121.14 116.81 4.33 1.75e+00 3.27e-01 6.13e+00 angle pdb=" C PHE A 601 " pdb=" N GLN A 602 " pdb=" CA GLN A 602 " ideal model delta sigma weight residual 121.14 116.81 4.33 1.75e+00 3.27e-01 6.12e+00 angle pdb=" N GLN B 619 " pdb=" CA GLN B 619 " pdb=" C GLN B 619 " ideal model delta sigma weight residual 113.72 110.18 3.54 1.52e+00 4.33e-01 5.43e+00 ... (remaining 18089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 7290 16.19 - 32.38: 410 32.38 - 48.57: 64 48.57 - 64.76: 16 64.76 - 80.95: 6 Dihedral angle restraints: 7786 sinusoidal: 3058 harmonic: 4728 Sorted by residual: dihedral pdb=" CA TYR A 617 " pdb=" C TYR A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA TYR B 617 " pdb=" C TYR B 617 " pdb=" N SER B 618 " pdb=" CA SER B 618 " ideal model delta harmonic sigma weight residual 180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA A 494 " pdb=" C ALA A 494 " pdb=" N GLU A 495 " pdb=" CA GLU A 495 " ideal model delta harmonic sigma weight residual -180.00 -161.96 -18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 7783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1137 0.025 - 0.050: 505 0.050 - 0.074: 226 0.074 - 0.099: 64 0.099 - 0.124: 52 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CA VAL B 348 " pdb=" N VAL B 348 " pdb=" C VAL B 348 " pdb=" CB VAL B 348 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA VAL A 348 " pdb=" N VAL A 348 " pdb=" C VAL A 348 " pdb=" CB VAL A 348 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE A 345 " pdb=" N ILE A 345 " pdb=" C ILE A 345 " pdb=" CB ILE A 345 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1981 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C PHE A 598 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 598 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C PHE B 598 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE B 598 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE B 599 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 599 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C ILE B 599 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE B 599 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 600 " 0.015 2.00e-02 2.50e+03 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2970 2.79 - 3.32: 11959 3.32 - 3.85: 20135 3.85 - 4.37: 21477 4.37 - 4.90: 40906 Nonbonded interactions: 97447 Sorted by model distance: nonbonded pdb=" OE2 GLU A 225 " pdb=" OH TYR B 52 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU B 225 " model vdw 2.275 3.040 nonbonded pdb=" O VAL A 726 " pdb=" OG1 THR A 730 " model vdw 2.359 3.040 nonbonded pdb=" O VAL B 726 " pdb=" OG1 THR B 730 " model vdw 2.360 3.040 nonbonded pdb=" OE1 GLU A 312 " pdb=" NH2 ARG B 773 " model vdw 2.367 3.120 ... (remaining 97442 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.870 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13324 Z= 0.134 Angle : 0.477 5.648 18094 Z= 0.261 Chirality : 0.038 0.124 1984 Planarity : 0.004 0.032 2290 Dihedral : 10.785 80.950 4750 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.29 % Allowed : 6.33 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.22), residues: 1606 helix: 2.66 (0.17), residues: 984 sheet: -0.16 (0.42), residues: 152 loop : -1.49 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 804 HIS 0.003 0.001 HIS B 578 PHE 0.013 0.001 PHE B 545 TYR 0.010 0.001 TYR B 460 ARG 0.002 0.000 ARG A 608 Details of bonding type rmsd hydrogen bonds : bond 0.13260 ( 834) hydrogen bonds : angle 5.21558 ( 2460) covalent geometry : bond 0.00274 (13324) covalent geometry : angle 0.47745 (18094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 210 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 652 MET cc_start: 0.7827 (mmm) cc_final: 0.7541 (mmm) REVERT: A 790 LYS cc_start: 0.7904 (mttm) cc_final: 0.7541 (tttm) REVERT: A 814 PHE cc_start: 0.8048 (m-10) cc_final: 0.7812 (t80) REVERT: B 513 MET cc_start: 0.8443 (mtp) cc_final: 0.8187 (mtp) REVERT: B 652 MET cc_start: 0.7959 (mmm) cc_final: 0.7683 (mmm) REVERT: B 733 SER cc_start: 0.8132 (t) cc_final: 0.7792 (m) REVERT: B 790 LYS cc_start: 0.7925 (mttm) cc_final: 0.7475 (tttm) REVERT: B 814 PHE cc_start: 0.7920 (m-10) cc_final: 0.7686 (t80) outliers start: 4 outliers final: 2 residues processed: 212 average time/residue: 0.2618 time to fit residues: 78.7090 Evaluate side-chains 117 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain B residue 327 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.089580 restraints weight = 19722.927| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.17 r_work: 0.2938 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13324 Z= 0.163 Angle : 0.527 5.725 18094 Z= 0.285 Chirality : 0.039 0.128 1984 Planarity : 0.004 0.039 2290 Dihedral : 4.257 36.152 1774 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.94 % Allowed : 11.37 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.22), residues: 1606 helix: 2.63 (0.17), residues: 996 sheet: 0.36 (0.42), residues: 164 loop : -1.46 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 804 HIS 0.003 0.001 HIS B 394 PHE 0.016 0.001 PHE A 545 TYR 0.010 0.001 TYR A 207 ARG 0.003 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.06941 ( 834) hydrogen bonds : angle 4.65711 ( 2460) covalent geometry : bond 0.00359 (13324) covalent geometry : angle 0.52698 (18094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 790 LYS cc_start: 0.8317 (mttm) cc_final: 0.7803 (tttm) REVERT: A 814 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7759 (t80) REVERT: B 193 MET cc_start: 0.8541 (mmm) cc_final: 0.8336 (mmm) REVERT: B 513 MET cc_start: 0.9102 (mtp) cc_final: 0.8821 (mtp) REVERT: B 652 MET cc_start: 0.7984 (mmm) cc_final: 0.7600 (mmm) REVERT: B 790 LYS cc_start: 0.8125 (mttm) cc_final: 0.7588 (tttm) REVERT: B 814 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7607 (t80) outliers start: 27 outliers final: 18 residues processed: 142 average time/residue: 0.2181 time to fit residues: 47.7742 Evaluate side-chains 128 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 848 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.090805 restraints weight = 19939.756| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.25 r_work: 0.2943 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13324 Z= 0.138 Angle : 0.496 7.252 18094 Z= 0.267 Chirality : 0.038 0.126 1984 Planarity : 0.004 0.033 2290 Dihedral : 4.199 37.494 1774 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.09 % Allowed : 12.30 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.22), residues: 1606 helix: 2.76 (0.17), residues: 996 sheet: 0.29 (0.41), residues: 166 loop : -1.50 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 804 HIS 0.002 0.001 HIS B 394 PHE 0.014 0.001 PHE B 545 TYR 0.010 0.001 TYR A 207 ARG 0.003 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.06447 ( 834) hydrogen bonds : angle 4.52544 ( 2460) covalent geometry : bond 0.00291 (13324) covalent geometry : angle 0.49625 (18094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 736 ASN cc_start: 0.8421 (m-40) cc_final: 0.8163 (m110) REVERT: A 790 LYS cc_start: 0.8321 (mttm) cc_final: 0.7698 (tttm) REVERT: A 794 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7935 (mm-30) REVERT: A 814 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7697 (t80) REVERT: B 193 MET cc_start: 0.8640 (mmm) cc_final: 0.8433 (mmm) REVERT: B 513 MET cc_start: 0.9096 (mtp) cc_final: 0.8878 (mtp) REVERT: B 540 LEU cc_start: 0.9141 (mt) cc_final: 0.8929 (mp) REVERT: B 790 LYS cc_start: 0.8066 (mttm) cc_final: 0.7642 (tttm) REVERT: B 814 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7610 (t80) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.2149 time to fit residues: 48.1884 Evaluate side-chains 134 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 814 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 45 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 156 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 0.0570 chunk 13 optimal weight: 5.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.092040 restraints weight = 19695.332| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.25 r_work: 0.2965 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13324 Z= 0.121 Angle : 0.483 7.191 18094 Z= 0.258 Chirality : 0.038 0.124 1984 Planarity : 0.004 0.031 2290 Dihedral : 4.122 38.561 1774 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.95 % Allowed : 13.02 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.22), residues: 1606 helix: 2.84 (0.17), residues: 998 sheet: 0.29 (0.41), residues: 166 loop : -1.51 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.002 0.001 HIS A 394 PHE 0.013 0.001 PHE B 545 TYR 0.010 0.001 TYR A 207 ARG 0.002 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.05946 ( 834) hydrogen bonds : angle 4.43656 ( 2460) covalent geometry : bond 0.00241 (13324) covalent geometry : angle 0.48342 (18094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: A 736 ASN cc_start: 0.8461 (m-40) cc_final: 0.8192 (m110) REVERT: A 737 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7306 (tt) REVERT: A 790 LYS cc_start: 0.8315 (mttm) cc_final: 0.7691 (tttm) REVERT: A 794 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7863 (mm-30) REVERT: A 814 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7652 (t80) REVERT: B 314 LEU cc_start: 0.8741 (tp) cc_final: 0.8463 (tp) REVERT: B 510 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8773 (p0) REVERT: B 513 MET cc_start: 0.9088 (mtp) cc_final: 0.8871 (mtp) REVERT: B 737 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7182 (tt) REVERT: B 790 LYS cc_start: 0.8093 (mttm) cc_final: 0.7586 (tttm) REVERT: B 814 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7594 (t80) outliers start: 41 outliers final: 25 residues processed: 163 average time/residue: 0.2528 time to fit residues: 61.4295 Evaluate side-chains 148 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 142 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.091167 restraints weight = 19804.561| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.18 r_work: 0.2969 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13324 Z= 0.122 Angle : 0.481 7.536 18094 Z= 0.256 Chirality : 0.037 0.124 1984 Planarity : 0.004 0.080 2290 Dihedral : 4.066 39.052 1774 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.02 % Allowed : 13.53 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.22), residues: 1606 helix: 2.88 (0.17), residues: 990 sheet: 0.25 (0.41), residues: 166 loop : -1.50 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.002 0.001 HIS B 430 PHE 0.020 0.001 PHE A 487 TYR 0.010 0.001 TYR A 207 ARG 0.003 0.000 ARG A 772 Details of bonding type rmsd hydrogen bonds : bond 0.05873 ( 834) hydrogen bonds : angle 4.40107 ( 2460) covalent geometry : bond 0.00249 (13324) covalent geometry : angle 0.48130 (18094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7250 (pp) REVERT: A 134 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8919 (mm-40) REVERT: A 510 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8669 (p0) REVERT: A 736 ASN cc_start: 0.8439 (m-40) cc_final: 0.8180 (m110) REVERT: A 737 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7321 (tt) REVERT: A 790 LYS cc_start: 0.8310 (mttm) cc_final: 0.7685 (tttm) REVERT: A 794 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7793 (mm-30) REVERT: A 814 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 39 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7111 (pp) REVERT: B 86 ARG cc_start: 0.7720 (ptm160) cc_final: 0.7297 (mtm110) REVERT: B 510 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8747 (p0) REVERT: B 737 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7144 (tt) REVERT: B 790 LYS cc_start: 0.8080 (mttm) cc_final: 0.7637 (tttm) REVERT: B 814 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7629 (t80) outliers start: 42 outliers final: 28 residues processed: 157 average time/residue: 0.2463 time to fit residues: 58.3233 Evaluate side-chains 153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 38 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 93 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.092475 restraints weight = 19859.018| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.20 r_work: 0.2980 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13324 Z= 0.118 Angle : 0.479 7.970 18094 Z= 0.255 Chirality : 0.037 0.123 1984 Planarity : 0.004 0.064 2290 Dihedral : 4.024 39.588 1774 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.17 % Allowed : 14.17 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.22), residues: 1606 helix: 2.92 (0.17), residues: 990 sheet: 0.29 (0.41), residues: 166 loop : -1.49 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.002 0.000 HIS B 430 PHE 0.013 0.001 PHE B 601 TYR 0.009 0.001 TYR A 207 ARG 0.003 0.000 ARG A 772 Details of bonding type rmsd hydrogen bonds : bond 0.05673 ( 834) hydrogen bonds : angle 4.37548 ( 2460) covalent geometry : bond 0.00236 (13324) covalent geometry : angle 0.47914 (18094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 134 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8907 (mm-40) REVERT: A 510 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8567 (p0) REVERT: A 736 ASN cc_start: 0.8414 (m-40) cc_final: 0.8130 (m110) REVERT: A 737 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7348 (tt) REVERT: A 790 LYS cc_start: 0.8317 (mttm) cc_final: 0.7820 (tttm) REVERT: A 814 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 39 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7089 (pp) REVERT: B 86 ARG cc_start: 0.7696 (ptm160) cc_final: 0.7257 (mtm110) REVERT: B 314 LEU cc_start: 0.8714 (tp) cc_final: 0.8464 (tp) REVERT: B 510 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8729 (p0) REVERT: B 737 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7133 (tt) REVERT: B 790 LYS cc_start: 0.8094 (mttm) cc_final: 0.7603 (tttm) REVERT: B 814 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7602 (t80) outliers start: 44 outliers final: 30 residues processed: 164 average time/residue: 0.2373 time to fit residues: 58.1051 Evaluate side-chains 153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 157 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 83 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092253 restraints weight = 19693.930| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.18 r_work: 0.2977 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13324 Z= 0.123 Angle : 0.482 8.516 18094 Z= 0.257 Chirality : 0.038 0.136 1984 Planarity : 0.004 0.055 2290 Dihedral : 4.010 39.683 1774 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.38 % Allowed : 14.68 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.22), residues: 1606 helix: 2.91 (0.17), residues: 1000 sheet: 0.26 (0.41), residues: 166 loop : -1.45 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.002 0.001 HIS B 430 PHE 0.013 0.001 PHE B 545 TYR 0.010 0.001 TYR A 207 ARG 0.003 0.000 ARG A 772 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 834) hydrogen bonds : angle 4.37237 ( 2460) covalent geometry : bond 0.00255 (13324) covalent geometry : angle 0.48239 (18094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7256 (pp) REVERT: A 134 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8913 (mm-40) REVERT: A 510 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8554 (p0) REVERT: A 736 ASN cc_start: 0.8416 (m-40) cc_final: 0.8126 (m110) REVERT: A 737 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7333 (tt) REVERT: A 790 LYS cc_start: 0.8326 (mttm) cc_final: 0.7812 (tttm) REVERT: A 814 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7654 (t80) REVERT: B 39 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7083 (pp) REVERT: B 86 ARG cc_start: 0.7735 (ptm160) cc_final: 0.7292 (mtm110) REVERT: B 737 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7159 (tt) REVERT: B 790 LYS cc_start: 0.8074 (mttm) cc_final: 0.7650 (tttm) REVERT: B 814 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7611 (t80) outliers start: 47 outliers final: 34 residues processed: 156 average time/residue: 0.2355 time to fit residues: 54.9562 Evaluate side-chains 153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 0.9980 chunk 121 optimal weight: 0.3980 chunk 9 optimal weight: 0.0570 chunk 108 optimal weight: 0.0020 chunk 132 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 overall best weight: 0.3106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN B 647 ASN B 736 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093969 restraints weight = 19773.596| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.20 r_work: 0.3005 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13324 Z= 0.109 Angle : 0.475 8.678 18094 Z= 0.251 Chirality : 0.037 0.131 1984 Planarity : 0.004 0.067 2290 Dihedral : 3.979 40.328 1774 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.17 % Allowed : 14.75 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.22), residues: 1606 helix: 2.99 (0.17), residues: 992 sheet: 0.34 (0.41), residues: 166 loop : -1.35 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.002 0.000 HIS A 851 PHE 0.014 0.001 PHE A 601 TYR 0.008 0.001 TYR A 207 ARG 0.003 0.000 ARG A 772 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 834) hydrogen bonds : angle 4.33620 ( 2460) covalent geometry : bond 0.00204 (13324) covalent geometry : angle 0.47452 (18094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7326 (pp) REVERT: A 134 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8914 (mm-40) REVERT: A 314 LEU cc_start: 0.8662 (tp) cc_final: 0.8454 (tp) REVERT: A 510 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8697 (p0) REVERT: A 736 ASN cc_start: 0.8392 (m-40) cc_final: 0.8104 (m110) REVERT: A 737 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7271 (tt) REVERT: A 790 LYS cc_start: 0.8305 (mttm) cc_final: 0.7796 (tttm) REVERT: A 814 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7631 (t80) REVERT: B 39 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7060 (pp) REVERT: B 86 ARG cc_start: 0.7808 (ptm160) cc_final: 0.7390 (mtm110) REVERT: B 314 LEU cc_start: 0.8698 (tp) cc_final: 0.8470 (tp) REVERT: B 510 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8714 (p0) REVERT: B 737 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7032 (tt) REVERT: B 790 LYS cc_start: 0.8101 (mttm) cc_final: 0.7687 (tttm) REVERT: B 814 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7568 (t80) outliers start: 44 outliers final: 29 residues processed: 162 average time/residue: 0.2705 time to fit residues: 65.5416 Evaluate side-chains 155 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091984 restraints weight = 19749.421| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.18 r_work: 0.2977 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13324 Z= 0.138 Angle : 0.494 8.835 18094 Z= 0.262 Chirality : 0.038 0.142 1984 Planarity : 0.004 0.083 2290 Dihedral : 3.988 39.809 1774 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.02 % Allowed : 14.89 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.22), residues: 1606 helix: 2.90 (0.17), residues: 1000 sheet: 0.26 (0.41), residues: 166 loop : -1.41 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 430 PHE 0.014 0.001 PHE B 545 TYR 0.015 0.001 TYR B 52 ARG 0.003 0.000 ARG A 772 Details of bonding type rmsd hydrogen bonds : bond 0.05803 ( 834) hydrogen bonds : angle 4.37332 ( 2460) covalent geometry : bond 0.00305 (13324) covalent geometry : angle 0.49409 (18094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7368 (pp) REVERT: A 134 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8920 (mm-40) REVERT: A 510 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8697 (p0) REVERT: A 736 ASN cc_start: 0.8415 (m-40) cc_final: 0.8124 (m110) REVERT: A 737 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7318 (tt) REVERT: A 790 LYS cc_start: 0.8327 (mttm) cc_final: 0.7822 (tttm) REVERT: A 814 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7657 (t80) REVERT: B 39 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7097 (pp) REVERT: B 86 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7374 (mtm110) REVERT: B 510 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8709 (p0) REVERT: B 737 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7261 (tt) REVERT: B 790 LYS cc_start: 0.8107 (mttm) cc_final: 0.7644 (tttm) REVERT: B 814 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7607 (t80) outliers start: 42 outliers final: 31 residues processed: 155 average time/residue: 0.2803 time to fit residues: 65.5441 Evaluate side-chains 155 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 68 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089878 restraints weight = 19897.193| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.16 r_work: 0.2939 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13324 Z= 0.175 Angle : 0.527 9.112 18094 Z= 0.282 Chirality : 0.039 0.139 1984 Planarity : 0.004 0.073 2290 Dihedral : 4.091 39.337 1774 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.81 % Allowed : 15.32 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.22), residues: 1606 helix: 2.81 (0.17), residues: 1002 sheet: 0.17 (0.41), residues: 166 loop : -1.47 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.003 0.001 HIS B 430 PHE 0.017 0.001 PHE B 545 TYR 0.014 0.001 TYR B 52 ARG 0.002 0.000 ARG A 772 Details of bonding type rmsd hydrogen bonds : bond 0.06479 ( 834) hydrogen bonds : angle 4.46451 ( 2460) covalent geometry : bond 0.00404 (13324) covalent geometry : angle 0.52680 (18094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7290 (pp) REVERT: A 134 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8915 (mm-40) REVERT: A 510 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8642 (p0) REVERT: A 737 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7426 (tt) REVERT: A 790 LYS cc_start: 0.8341 (mttm) cc_final: 0.7852 (tttm) REVERT: A 814 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7758 (t80) REVERT: A 856 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6302 (mmm160) REVERT: B 39 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7157 (pp) REVERT: B 510 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8689 (p0) REVERT: B 737 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7319 (tt) REVERT: B 790 LYS cc_start: 0.8127 (mttm) cc_final: 0.7702 (tttm) REVERT: B 814 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7700 (t80) outliers start: 39 outliers final: 29 residues processed: 150 average time/residue: 0.3617 time to fit residues: 81.4466 Evaluate side-chains 149 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 814 PHE Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN B 109 ASN B 420 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.090108 restraints weight = 19830.691| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.18 r_work: 0.2933 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13324 Z= 0.147 Angle : 0.508 9.272 18094 Z= 0.273 Chirality : 0.039 0.133 1984 Planarity : 0.004 0.066 2290 Dihedral : 4.111 40.292 1774 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.81 % Allowed : 15.61 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.22), residues: 1606 helix: 2.80 (0.17), residues: 1002 sheet: 0.15 (0.41), residues: 166 loop : -1.40 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.002 0.001 HIS A 394 PHE 0.015 0.001 PHE A 545 TYR 0.014 0.001 TYR B 52 ARG 0.002 0.000 ARG A 779 Details of bonding type rmsd hydrogen bonds : bond 0.06318 ( 834) hydrogen bonds : angle 4.45651 ( 2460) covalent geometry : bond 0.00324 (13324) covalent geometry : angle 0.50828 (18094) =============================================================================== Job complete usr+sys time: 6824.86 seconds wall clock time: 119 minutes 39.80 seconds (7179.80 seconds total)