Starting phenix.real_space_refine on Mon Dec 30 08:08:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wjm_32545/12_2024/7wjm_32545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wjm_32545/12_2024/7wjm_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_32545/12_2024/7wjm_32545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wjm_32545/12_2024/7wjm_32545.map" model { file = "/net/cci-nas-00/data/ceres_data/7wjm_32545/12_2024/7wjm_32545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wjm_32545/12_2024/7wjm_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 13.62, per 1000 atoms: 1.05 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 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: 1.38 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: 4.59 Time building geometry restraints manager: 3.73 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: 0.00 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: 1.170 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.090 Find NCS groups from input model: 0.590 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- 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= 0.180 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 *********************** 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 : 1.532 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: 0.2745 time to fit residues: 82.5096 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 : 1.619 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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= 0.235 Angle : 0.527 5.726 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 *********************** 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 : 1.499 Fit side-chains revert: symmetry clash REVERT: A 790 LYS cc_start: 0.7981 (mttm) cc_final: 0.7593 (tttm) REVERT: A 814 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7772 (t80) REVERT: B 193 MET cc_start: 0.8370 (mmm) cc_final: 0.8158 (mmm) REVERT: B 513 MET cc_start: 0.8459 (mtp) cc_final: 0.8188 (mtp) REVERT: B 652 MET cc_start: 0.7758 (mmm) cc_final: 0.7401 (mmm) REVERT: B 790 LYS cc_start: 0.7802 (mttm) cc_final: 0.7380 (tttm) REVERT: B 814 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7647 (t80) outliers start: 27 outliers final: 18 residues processed: 142 average time/residue: 0.2282 time to fit residues: 49.7796 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 : 1.639 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.0970 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1438 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= 0.159 Angle : 0.481 6.635 18094 Z= 0.259 Chirality : 0.038 0.122 1984 Planarity : 0.004 0.031 2290 Dihedral : 4.142 37.943 1774 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.23 % Allowed : 12.16 % 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: 2.18 (0.22), residues: 1606 helix: 2.80 (0.17), residues: 998 sheet: 0.35 (0.41), residues: 166 loop : -1.46 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.002 0.000 HIS B 394 PHE 0.013 0.001 PHE B 545 TYR 0.009 0.001 TYR B 460 ARG 0.003 0.000 ARG A 785 *********************** 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 158 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.470 Fit side-chains REVERT: A 790 LYS cc_start: 0.7957 (mttm) cc_final: 0.7469 (tttm) REVERT: A 814 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7718 (t80) REVERT: B 193 MET cc_start: 0.8424 (mmm) cc_final: 0.8215 (mmm) REVERT: B 513 MET cc_start: 0.8438 (mtp) cc_final: 0.8179 (mtp) REVERT: B 790 LYS cc_start: 0.7780 (mttm) cc_final: 0.7437 (tttm) REVERT: B 814 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7600 (t80) outliers start: 31 outliers final: 17 residues processed: 153 average time/residue: 0.2391 time to fit residues: 55.4796 Evaluate side-chains 132 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 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 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 143 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 0.0020 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8590 ------------------------------------------------------------------------------- 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 ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13324 Z= 0.191 Angle : 0.495 7.557 18094 Z= 0.265 Chirality : 0.038 0.126 1984 Planarity : 0.004 0.032 2290 Dihedral : 4.142 37.765 1774 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.95 % Allowed : 12.66 % Favored : 84.39 % 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: 2.82 (0.17), residues: 998 sheet: 0.25 (0.41), residues: 166 loop : -1.45 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 804 HIS 0.002 0.001 HIS B 394 PHE 0.021 0.001 PHE A 487 TYR 0.011 0.001 TYR B 207 ARG 0.003 0.000 ARG A 772 *********************** 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 160 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: A 737 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7173 (tt) REVERT: A 790 LYS cc_start: 0.7761 (mttm) cc_final: 0.7447 (tttm) REVERT: A 814 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7724 (t80) REVERT: B 513 MET cc_start: 0.8402 (mtp) cc_final: 0.8163 (mtp) REVERT: B 737 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6940 (tt) REVERT: B 790 LYS cc_start: 0.7760 (mttm) cc_final: 0.7425 (tttm) REVERT: B 814 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7650 (t80) outliers start: 41 outliers final: 28 residues processed: 155 average time/residue: 0.2493 time to fit residues: 57.8417 Evaluate side-chains 146 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 347 THR 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 688 ILE 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 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 688 ILE 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 128 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 420 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13324 Z= 0.286 Angle : 0.543 7.536 18094 Z= 0.291 Chirality : 0.040 0.136 1984 Planarity : 0.004 0.079 2290 Dihedral : 4.280 38.078 1774 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.74 % Allowed : 12.95 % Favored : 83.31 % 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: 2.69 (0.17), residues: 1000 sheet: 0.04 (0.40), residues: 166 loop : -1.53 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 804 HIS 0.003 0.001 HIS A 394 PHE 0.017 0.001 PHE A 545 TYR 0.015 0.001 TYR B 207 ARG 0.002 0.000 ARG B 103 *********************** 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 163 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 111 time to evaluate : 1.521 Fit side-chains REVERT: A 39 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7148 (pp) REVERT: A 134 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8945 (mm-40) REVERT: A 510 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8647 (p0) REVERT: A 737 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7236 (tt) REVERT: A 790 LYS cc_start: 0.7832 (mttm) cc_final: 0.7546 (tttm) REVERT: A 814 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7824 (t80) REVERT: A 856 ARG cc_start: 0.6783 (ttt180) cc_final: 0.6456 (mmm160) REVERT: B 39 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7143 (pp) REVERT: B 510 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8711 (p0) REVERT: B 513 MET cc_start: 0.8448 (mtp) cc_final: 0.8244 (mtp) REVERT: B 737 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7118 (tt) REVERT: B 790 LYS cc_start: 0.7808 (mttm) cc_final: 0.7461 (tttm) REVERT: B 814 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7769 (t80) outliers start: 52 outliers final: 37 residues processed: 157 average time/residue: 0.2487 time to fit residues: 58.6013 Evaluate side-chains 150 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 688 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 697 VAL 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 87 THR 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 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 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 697 VAL 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 52 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 154 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 0.0670 overall best weight: 0.3428 ------------------------------------------------------------------------------- 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 109 ASN B 420 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13324 Z= 0.136 Angle : 0.470 6.779 18094 Z= 0.252 Chirality : 0.037 0.140 1984 Planarity : 0.004 0.062 2290 Dihedral : 4.133 41.454 1774 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.88 % Allowed : 14.96 % Favored : 82.16 % 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: 2.33 (0.22), residues: 1606 helix: 2.99 (0.17), residues: 980 sheet: 0.32 (0.41), residues: 166 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 539 HIS 0.001 0.000 HIS B 651 PHE 0.013 0.001 PHE A 601 TYR 0.013 0.001 TYR B 52 ARG 0.003 0.000 ARG A 772 *********************** 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 164 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.397 Fit side-chains REVERT: A 86 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7414 (mtm110) REVERT: A 510 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8701 (p0) REVERT: A 737 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7130 (tt) REVERT: A 790 LYS cc_start: 0.7827 (mttm) cc_final: 0.7536 (tttm) REVERT: A 814 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7683 (t80) REVERT: A 856 ARG cc_start: 0.6668 (ttt180) cc_final: 0.6344 (mmm160) REVERT: B 39 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7064 (pp) REVERT: B 314 LEU cc_start: 0.8457 (tp) cc_final: 0.8252 (tp) REVERT: B 510 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8729 (p0) REVERT: B 737 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7007 (tt) REVERT: B 790 LYS cc_start: 0.7766 (mttm) cc_final: 0.7444 (tttm) REVERT: B 814 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7668 (t80) outliers start: 40 outliers final: 24 residues processed: 159 average time/residue: 0.2385 time to fit residues: 56.9622 Evaluate side-chains 144 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 420 ASN 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 684 THR 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 671 SER Chi-restraints excluded: chain B residue 684 THR 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 149 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1868 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= 0.204 Angle : 0.499 7.402 18094 Z= 0.267 Chirality : 0.038 0.126 1984 Planarity : 0.004 0.070 2290 Dihedral : 4.093 40.087 1774 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.73 % Allowed : 15.25 % Favored : 82.01 % 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: 2.89 (0.17), residues: 1000 sheet: 0.27 (0.41), residues: 166 loop : -1.42 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 804 HIS 0.002 0.001 HIS B 430 PHE 0.014 0.001 PHE A 545 TYR 0.011 0.001 TYR B 52 ARG 0.003 0.000 ARG A 772 *********************** 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 151 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7927 (ptm160) cc_final: 0.7423 (mtm110) REVERT: A 510 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8535 (p0) REVERT: A 737 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7178 (tt) REVERT: A 790 LYS cc_start: 0.7833 (mttm) cc_final: 0.7573 (tttm) REVERT: A 814 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7723 (t80) REVERT: A 856 ARG cc_start: 0.6713 (ttt180) cc_final: 0.6379 (mmm160) REVERT: B 39 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7113 (pp) REVERT: B 510 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8724 (p0) REVERT: B 737 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7053 (tt) REVERT: B 790 LYS cc_start: 0.7814 (mttm) cc_final: 0.7466 (tttm) REVERT: B 814 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7709 (t80) outliers start: 38 outliers final: 26 residues processed: 146 average time/residue: 0.2662 time to fit residues: 58.2377 Evaluate side-chains 144 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 98 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13324 Z= 0.160 Angle : 0.490 8.564 18094 Z= 0.260 Chirality : 0.038 0.123 1984 Planarity : 0.004 0.060 2290 Dihedral : 4.065 40.760 1774 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.73 % Allowed : 15.47 % Favored : 81.80 % 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: 2.88 (0.17), residues: 1002 sheet: 0.31 (0.41), residues: 166 loop : -1.43 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 804 HIS 0.002 0.001 HIS A 430 PHE 0.013 0.001 PHE A 545 TYR 0.011 0.001 TYR B 52 ARG 0.003 0.000 ARG A 772 *********************** 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 152 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7472 (mtm110) REVERT: A 510 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8675 (p0) REVERT: A 737 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7110 (tt) REVERT: A 790 LYS cc_start: 0.7894 (mttm) cc_final: 0.7617 (tttm) REVERT: A 814 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7709 (t80) REVERT: A 856 ARG cc_start: 0.6703 (ttt180) cc_final: 0.6363 (mmm160) REVERT: B 39 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7036 (pp) REVERT: B 510 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8707 (p0) REVERT: B 737 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7046 (tt) REVERT: B 790 LYS cc_start: 0.7798 (mttm) cc_final: 0.7482 (tttm) REVERT: B 814 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7701 (t80) outliers start: 38 outliers final: 24 residues processed: 147 average time/residue: 0.2694 time to fit residues: 59.0495 Evaluate side-chains 141 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 510 ASN Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 548 LEU 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 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 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 140 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13324 Z= 0.184 Angle : 0.503 8.530 18094 Z= 0.266 Chirality : 0.038 0.126 1984 Planarity : 0.004 0.081 2290 Dihedral : 4.053 40.496 1774 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.73 % Allowed : 15.32 % 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: 2.24 (0.22), residues: 1606 helix: 2.86 (0.17), residues: 1002 sheet: 0.24 (0.41), residues: 166 loop : -1.47 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 804 HIS 0.002 0.001 HIS B 430 PHE 0.013 0.001 PHE A 601 TYR 0.010 0.001 TYR B 207 ARG 0.003 0.000 ARG A 772 *********************** 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 150 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7476 (mtm110) REVERT: A 510 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8672 (p0) REVERT: A 737 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7132 (tt) REVERT: A 790 LYS cc_start: 0.7923 (mttm) cc_final: 0.7624 (tttm) REVERT: A 814 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 856 ARG cc_start: 0.6724 (ttt180) cc_final: 0.6376 (mmm160) REVERT: B 39 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7074 (pp) REVERT: B 510 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8677 (p0) REVERT: B 737 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7055 (tt) REVERT: B 790 LYS cc_start: 0.7806 (mttm) cc_final: 0.7476 (tttm) REVERT: B 814 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7706 (t80) outliers start: 38 outliers final: 26 residues processed: 145 average time/residue: 0.2599 time to fit residues: 55.8906 Evaluate side-chains 145 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 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 566 VAL Chi-restraints excluded: chain B residue 671 SER 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 151 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 0.0770 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13324 Z= 0.148 Angle : 0.480 8.567 18094 Z= 0.253 Chirality : 0.038 0.121 1984 Planarity : 0.004 0.072 2290 Dihedral : 3.995 41.511 1774 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.45 % Allowed : 15.68 % 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: 2.29 (0.22), residues: 1606 helix: 2.89 (0.17), residues: 1002 sheet: 0.35 (0.42), residues: 162 loop : -1.44 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.002 0.000 HIS B 514 PHE 0.014 0.001 PHE A 601 TYR 0.010 0.001 TYR B 52 ARG 0.002 0.000 ARG A 772 ********************** 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 154 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7945 (ptm160) cc_final: 0.7468 (mtm110) REVERT: A 510 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8659 (p0) REVERT: A 737 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7090 (tt) REVERT: A 790 LYS cc_start: 0.7896 (mttm) cc_final: 0.7647 (tttm) REVERT: A 814 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7655 (t80) REVERT: A 856 ARG cc_start: 0.6690 (ttt180) cc_final: 0.6349 (mmm160) REVERT: B 39 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7150 (pp) REVERT: B 510 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8652 (p0) REVERT: B 737 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7077 (tt) REVERT: B 790 LYS cc_start: 0.7879 (mttm) cc_final: 0.7571 (tttm) REVERT: B 814 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7602 (t80) outliers start: 34 outliers final: 25 residues processed: 150 average time/residue: 0.2648 time to fit residues: 58.2691 Evaluate side-chains 150 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 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 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 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 135 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 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 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 = 0.3438 r_free = 0.3438 target = 0.117379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090911 restraints weight = 19772.096| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.16 r_work: 0.2954 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13324 Z= 0.219 Angle : 0.518 8.289 18094 Z= 0.274 Chirality : 0.039 0.129 1984 Planarity : 0.004 0.064 2290 Dihedral : 4.044 40.300 1774 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 2.52 % Allowed : 15.76 % Favored : 81.73 % 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: 2.21 (0.22), residues: 1606 helix: 2.85 (0.17), residues: 1002 sheet: 0.20 (0.41), residues: 166 loop : -1.48 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 804 HIS 0.004 0.001 HIS B 514 PHE 0.014 0.001 PHE B 545 TYR 0.012 0.001 TYR B 207 ARG 0.002 0.000 ARG B 461 =============================================================================== Job complete usr+sys time: 2605.94 seconds wall clock time: 48 minutes 22.46 seconds (2902.46 seconds total)