Starting phenix.real_space_refine on Mon Dec 30 09:57:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wjn_32546/12_2024/7wjn_32546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wjn_32546/12_2024/7wjn_32546.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/7wjn_32546/12_2024/7wjn_32546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wjn_32546/12_2024/7wjn_32546.map" model { file = "/net/cci-nas-00/data/ceres_data/7wjn_32546/12_2024/7wjn_32546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wjn_32546/12_2024/7wjn_32546.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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 74 5.16 5 C 8458 2.51 5 N 2170 2.21 5 O 2346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13054 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6487 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 30, 'TRANS': 777} Chain breaks: 2 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MN': 1, 'UD1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 14.32, per 1000 atoms: 1.10 Number of scatterers: 13054 At special positions: 0 Unit cell: (118.77, 112.35, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 74 16.00 P 4 15.00 O 2346 8.00 N 2170 7.00 C 8458 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: 3.70 Conformation dependent library (CDL) restraints added in 1.6 seconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 4 sheets defined 66.8% alpha, 8.9% 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 23 through 37 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.835A pdb=" N ASP A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.764A pdb=" N SER A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.146A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 163 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 262 removed outlier: 3.940A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (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: 3.560A pdb=" N HIS A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.562A pdb=" N SER A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 479 removed outlier: 5.156A pdb=" N THR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.666A pdb=" N LEU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.695A pdb=" N GLY A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 528 through 554 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.650A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 621 through 646 removed outlier: 4.235A 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 706 removed outlier: 5.302A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 5.368A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 735 Processing helix chain 'A' and resid 764 through 819 removed outlier: 3.581A pdb=" N PHE A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 853 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.779A pdb=" N GLY A 857 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.835A pdb=" N ASP B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.763A pdb=" N SER B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 112 through 134 removed outlier: 4.145A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 163 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 262 removed outlier: 3.941A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (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: 3.561A pdb=" N HIS B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.561A pdb=" N SER B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 479 removed outlier: 5.156A pdb=" N THR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 477 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.665A pdb=" N LEU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 493 removed outlier: 3.694A pdb=" N GLY B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 528 through 554 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 587 removed outlier: 3.650A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 605 Processing helix chain 'B' and resid 621 through 646 removed outlier: 4.235A 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 706 removed outlier: 5.301A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.367A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 735 Processing helix chain 'B' and resid 764 through 819 removed outlier: 3.580A pdb=" N PHE B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 853 Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.779A pdb=" N GLY B 857 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG B 858 " --> pdb=" O LEU B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 854 through 858' Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 6.049A pdb=" N HIS B 175 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 352 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS B 514 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.346A 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: 4.760A pdb=" N GLY B 410 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASP B 518 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LEU B 412 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 520 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL B 414 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.728A 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: 7.645A pdb=" N HIS A 514 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 408 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 516 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY A 410 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP A 518 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LEU A 412 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 520 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL A 414 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 522 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 352 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N HIS A 175 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 174 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER B 55 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.017A 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 337 855 hydrogen bonds defined for protein. 2517 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: 4.33 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4088 1.34 - 1.46: 2260 1.46 - 1.57: 6932 1.57 - 1.69: 6 1.69 - 1.81: 118 Bond restraints: 13404 Sorted by residual: bond pdb=" O1' UD1 A1001 " pdb=" PB UD1 A1001 " ideal model delta sigma weight residual 1.658 1.563 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O1' UD1 B1001 " pdb=" PB UD1 B1001 " ideal model delta sigma weight residual 1.658 1.563 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O5B UD1 B1001 " pdb=" PA UD1 B1001 " ideal model delta sigma weight residual 1.645 1.582 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O5B UD1 A1001 " pdb=" PA UD1 A1001 " ideal model delta sigma weight residual 1.645 1.582 0.063 2.00e-02 2.50e+03 9.81e+00 bond pdb=" O3A UD1 B1001 " pdb=" PA UD1 B1001 " ideal model delta sigma weight residual 1.642 1.586 0.056 2.00e-02 2.50e+03 7.89e+00 ... (remaining 13399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 18154 3.84 - 7.69: 46 7.69 - 11.53: 2 11.53 - 15.38: 2 15.38 - 19.22: 2 Bond angle restraints: 18206 Sorted by residual: angle pdb=" O1' UD1 A1001 " pdb=" PB UD1 A1001 " pdb=" O3A UD1 A1001 " ideal model delta sigma weight residual 92.88 112.10 -19.22 3.00e+00 1.11e-01 4.10e+01 angle pdb=" O1' UD1 B1001 " pdb=" PB UD1 B1001 " pdb=" O3A UD1 B1001 " ideal model delta sigma weight residual 92.88 112.10 -19.22 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PA UD1 B1001 " pdb=" O3A UD1 B1001 " pdb=" PB UD1 B1001 " ideal model delta sigma weight residual 122.84 137.31 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" PA UD1 A1001 " pdb=" O3A UD1 A1001 " pdb=" PB UD1 A1001 " ideal model delta sigma weight residual 122.84 137.29 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C SER A 615 " pdb=" N GLU A 616 " pdb=" CA GLU A 616 " ideal model delta sigma weight residual 121.71 116.60 5.11 1.39e+00 5.18e-01 1.35e+01 ... (remaining 18201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.93: 7316 14.93 - 29.86: 467 29.86 - 44.80: 89 44.80 - 59.73: 18 59.73 - 74.66: 6 Dihedral angle restraints: 7896 sinusoidal: 3162 harmonic: 4734 Sorted by residual: dihedral pdb=" CA GLN A 602 " pdb=" C GLN A 602 " pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLN B 602 " pdb=" C GLN B 602 " pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASN A 607 " pdb=" CB ASN A 607 " pdb=" CG ASN A 607 " pdb=" OD1 ASN A 607 " ideal model delta sinusoidal sigma weight residual -90.00 -153.48 63.48 2 2.00e+01 2.50e-03 9.61e+00 ... (remaining 7893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1623 0.047 - 0.095: 314 0.095 - 0.142: 63 0.142 - 0.189: 0 0.189 - 0.237: 2 Chirality restraints: 2002 Sorted by residual: chirality pdb=" C1B UD1 A1001 " pdb=" C2B UD1 A1001 " pdb=" N1 UD1 A1001 " pdb=" O4B UD1 A1001 " both_signs ideal model delta sigma weight residual False 2.20 2.44 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1B UD1 B1001 " pdb=" C2B UD1 B1001 " pdb=" N1 UD1 B1001 " pdb=" O4B UD1 B1001 " both_signs ideal model delta sigma weight residual False 2.20 2.44 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' UD1 A1001 " pdb=" C2' UD1 A1001 " pdb=" O1' UD1 A1001 " pdb=" O5' UD1 A1001 " both_signs ideal model delta sigma weight residual False -2.21 -2.34 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1999 not shown) Planarity restraints: 2292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 437 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C ASN A 437 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN A 437 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 438 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 437 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ASN B 437 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN B 437 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 438 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C PHE A 598 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.013 2.00e-02 2.50e+03 ... (remaining 2289 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2328 2.77 - 3.30: 12056 3.30 - 3.83: 21093 3.83 - 4.37: 22778 4.37 - 4.90: 42685 Nonbonded interactions: 100940 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU B 225 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASN A 109 " pdb=" NH2 ARG A 171 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASN B 109 " pdb=" NH2 ARG B 171 " model vdw 2.249 3.120 nonbonded pdb=" O GLU A 241 " pdb=" OG1 THR A 300 " model vdw 2.303 3.040 nonbonded pdb=" O GLU B 241 " pdb=" OG1 THR B 300 " model vdw 2.303 3.040 ... (remaining 100935 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: 2.150 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 38.030 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 13404 Z= 0.229 Angle : 0.586 19.220 18206 Z= 0.286 Chirality : 0.039 0.237 2002 Planarity : 0.004 0.043 2292 Dihedral : 10.438 74.658 4856 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.58 % Allowed : 5.33 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.22), residues: 1604 helix: 2.65 (0.17), residues: 1006 sheet: -0.26 (0.41), residues: 166 loop : -1.19 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 804 HIS 0.002 0.001 HIS B 578 PHE 0.012 0.001 PHE A 601 TYR 0.008 0.001 TYR A 365 ARG 0.003 0.000 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 250 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.6085 (mt) REVERT: A 327 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8239 (m-70) REVERT: A 738 GLN cc_start: 0.8155 (pm20) cc_final: 0.7368 (pm20) REVERT: A 785 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7020 (ttp80) REVERT: B 183 ASN cc_start: 0.7150 (m-40) cc_final: 0.6804 (p0) REVERT: B 403 HIS cc_start: 0.6931 (t-90) cc_final: 0.6641 (t-90) REVERT: B 552 TRP cc_start: 0.7593 (t-100) cc_final: 0.5244 (m-10) REVERT: B 790 LYS cc_start: 0.8149 (tttt) cc_final: 0.7920 (tttp) outliers start: 8 outliers final: 5 residues processed: 258 average time/residue: 0.2683 time to fit residues: 99.7633 Evaluate side-chains 157 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 478 ASN A 607 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN B 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13404 Z= 0.188 Angle : 0.501 7.674 18206 Z= 0.264 Chirality : 0.038 0.135 2002 Planarity : 0.004 0.045 2292 Dihedral : 6.803 59.305 1898 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.95 % Allowed : 9.37 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.22), residues: 1604 helix: 2.61 (0.17), residues: 1012 sheet: -0.39 (0.42), residues: 170 loop : -0.98 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 804 HIS 0.002 0.001 HIS A 578 PHE 0.014 0.001 PHE A 601 TYR 0.008 0.001 TYR A 732 ARG 0.005 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6354 (OUTLIER) cc_final: 0.5992 (mt) REVERT: A 71 MET cc_start: 0.0849 (ttm) cc_final: 0.0341 (mtt) REVERT: A 738 GLN cc_start: 0.8365 (pm20) cc_final: 0.7465 (pm20) REVERT: A 785 ARG cc_start: 0.7552 (ttm110) cc_final: 0.6785 (ttp80) REVERT: B 75 MET cc_start: 0.3204 (mpp) cc_final: 0.2763 (tpt) REVERT: B 183 ASN cc_start: 0.7131 (m-40) cc_final: 0.6828 (p0) REVERT: B 229 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7305 (mtm-85) REVERT: B 552 TRP cc_start: 0.7679 (t-100) cc_final: 0.5247 (m-10) REVERT: B 666 MET cc_start: 0.8237 (ttp) cc_final: 0.8016 (ttm) REVERT: B 780 ARG cc_start: 0.7040 (mtm110) cc_final: 0.6646 (ptp-110) REVERT: B 790 LYS cc_start: 0.8118 (tttt) cc_final: 0.7895 (tttp) outliers start: 27 outliers final: 10 residues processed: 183 average time/residue: 0.2596 time to fit residues: 69.5105 Evaluate side-chains 154 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 0.0060 chunk 157 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13404 Z= 0.186 Angle : 0.491 11.580 18206 Z= 0.257 Chirality : 0.038 0.133 2002 Planarity : 0.004 0.049 2292 Dihedral : 6.636 63.382 1894 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.09 % Allowed : 10.59 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1604 helix: 2.64 (0.17), residues: 1000 sheet: -0.52 (0.41), residues: 174 loop : -0.94 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.003 0.001 HIS A 327 PHE 0.024 0.001 PHE B 397 TYR 0.010 0.001 TYR A 219 ARG 0.008 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.797 Fit side-chains REVERT: A 37 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5962 (mt) REVERT: A 71 MET cc_start: 0.0811 (ttm) cc_final: 0.0380 (mtt) REVERT: A 161 ILE cc_start: 0.8409 (tp) cc_final: 0.8081 (tt) REVERT: A 229 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7335 (mtm-85) REVERT: B 75 MET cc_start: 0.3474 (mpp) cc_final: 0.3140 (tpt) REVERT: B 133 ARG cc_start: 0.6164 (mtt180) cc_final: 0.5889 (mtm-85) REVERT: B 183 ASN cc_start: 0.7133 (m-40) cc_final: 0.6901 (p0) REVERT: B 229 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7333 (mtm-85) REVERT: B 371 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7511 (mm-30) REVERT: B 552 TRP cc_start: 0.7623 (t-100) cc_final: 0.5003 (m-10) outliers start: 29 outliers final: 17 residues processed: 174 average time/residue: 0.2647 time to fit residues: 67.3396 Evaluate side-chains 162 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.0010 chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13404 Z= 0.150 Angle : 0.468 9.116 18206 Z= 0.246 Chirality : 0.037 0.130 2002 Planarity : 0.004 0.047 2292 Dihedral : 6.483 63.784 1894 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.89 % Rotamer: Outliers : 2.31 % Allowed : 11.31 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.22), residues: 1604 helix: 2.68 (0.17), residues: 1000 sheet: -0.48 (0.41), residues: 174 loop : -0.92 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 804 HIS 0.003 0.000 HIS A 327 PHE 0.019 0.001 PHE B 397 TYR 0.007 0.001 TYR B 492 ARG 0.006 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.664 Fit side-chains REVERT: A 37 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5969 (mt) REVERT: A 71 MET cc_start: 0.0801 (ttm) cc_final: 0.0396 (mtt) REVERT: A 161 ILE cc_start: 0.8427 (tp) cc_final: 0.8106 (tt) REVERT: A 229 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7270 (mtm-85) REVERT: A 651 HIS cc_start: 0.6790 (OUTLIER) cc_final: 0.5347 (p-80) REVERT: B 75 MET cc_start: 0.3702 (mpp) cc_final: 0.3214 (tpt) REVERT: B 183 ASN cc_start: 0.7111 (m-40) cc_final: 0.6909 (p0) REVERT: B 371 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7477 (mm-30) REVERT: B 552 TRP cc_start: 0.7630 (t-100) cc_final: 0.4998 (m-10) REVERT: B 651 HIS cc_start: 0.6456 (OUTLIER) cc_final: 0.5378 (p-80) REVERT: B 780 ARG cc_start: 0.6944 (mtm110) cc_final: 0.6463 (ptp-110) outliers start: 32 outliers final: 18 residues processed: 179 average time/residue: 0.2680 time to fit residues: 71.4120 Evaluate side-chains 163 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 106 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13404 Z= 0.172 Angle : 0.484 11.077 18206 Z= 0.251 Chirality : 0.038 0.128 2002 Planarity : 0.004 0.047 2292 Dihedral : 6.341 63.136 1894 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 2.31 % Allowed : 12.68 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1604 helix: 2.65 (0.17), residues: 1000 sheet: -0.50 (0.41), residues: 174 loop : -0.94 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.002 0.001 HIS B 578 PHE 0.017 0.001 PHE B 397 TYR 0.009 0.001 TYR B 239 ARG 0.007 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.453 Fit side-chains REVERT: A 37 ILE cc_start: 0.6359 (OUTLIER) cc_final: 0.6073 (mt) REVERT: A 71 MET cc_start: 0.0635 (ttm) cc_final: 0.0223 (mtt) REVERT: A 161 ILE cc_start: 0.8539 (tp) cc_final: 0.8269 (tt) REVERT: A 229 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7285 (mtm-85) REVERT: A 651 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.5268 (p-80) REVERT: B 75 MET cc_start: 0.3671 (mpp) cc_final: 0.3091 (tpt) REVERT: B 183 ASN cc_start: 0.7124 (m-40) cc_final: 0.6922 (p0) REVERT: B 229 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7274 (mtm-85) REVERT: B 371 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 552 TRP cc_start: 0.7641 (t-100) cc_final: 0.5021 (m-10) REVERT: B 651 HIS cc_start: 0.6468 (OUTLIER) cc_final: 0.5335 (p-80) outliers start: 32 outliers final: 22 residues processed: 176 average time/residue: 0.2524 time to fit residues: 66.2476 Evaluate side-chains 172 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8022 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13404 Z= 0.215 Angle : 0.499 8.717 18206 Z= 0.263 Chirality : 0.038 0.129 2002 Planarity : 0.004 0.047 2292 Dihedral : 6.358 62.034 1894 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.95 % Allowed : 12.90 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.22), residues: 1604 helix: 2.59 (0.17), residues: 1000 sheet: -0.50 (0.41), residues: 174 loop : -0.98 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 PHE 0.014 0.001 PHE B 601 TYR 0.011 0.001 TYR A 492 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.378 Fit side-chains REVERT: A 37 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.6027 (mt) REVERT: A 161 ILE cc_start: 0.8545 (tp) cc_final: 0.8249 (tt) REVERT: A 229 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7297 (mtm-85) REVERT: A 651 HIS cc_start: 0.6856 (OUTLIER) cc_final: 0.5427 (p-80) REVERT: B 75 MET cc_start: 0.3636 (mpp) cc_final: 0.3110 (tpt) REVERT: B 183 ASN cc_start: 0.7218 (m-40) cc_final: 0.6989 (p0) REVERT: B 229 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7320 (mtm-85) REVERT: B 371 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 552 TRP cc_start: 0.7667 (t-100) cc_final: 0.4809 (m-10) REVERT: B 651 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.5436 (p-80) outliers start: 41 outliers final: 29 residues processed: 177 average time/residue: 0.2339 time to fit residues: 61.7816 Evaluate side-chains 176 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8008 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13404 Z= 0.184 Angle : 0.492 10.829 18206 Z= 0.257 Chirality : 0.038 0.134 2002 Planarity : 0.004 0.048 2292 Dihedral : 6.289 61.412 1894 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.67 % Allowed : 13.26 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.22), residues: 1604 helix: 2.62 (0.17), residues: 1000 sheet: -0.44 (0.41), residues: 174 loop : -0.97 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 PHE 0.014 0.001 PHE B 545 TYR 0.008 0.001 TYR B 239 ARG 0.007 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.536 Fit side-chains REVERT: A 37 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6267 (mt) REVERT: A 161 ILE cc_start: 0.8510 (tp) cc_final: 0.8215 (tt) REVERT: A 229 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7307 (mtm-85) REVERT: A 651 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.5538 (p-80) REVERT: B 75 MET cc_start: 0.3560 (mpp) cc_final: 0.3041 (tpt) REVERT: B 183 ASN cc_start: 0.7252 (m-40) cc_final: 0.7026 (p0) REVERT: B 229 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7310 (mtm-85) REVERT: B 371 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7694 (mm-30) REVERT: B 552 TRP cc_start: 0.7699 (t-100) cc_final: 0.4953 (m-10) REVERT: B 651 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.5386 (p-80) REVERT: B 667 MET cc_start: 0.7899 (tpp) cc_final: 0.7550 (tpt) outliers start: 37 outliers final: 28 residues processed: 168 average time/residue: 0.2643 time to fit residues: 66.2462 Evaluate side-chains 167 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8030 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13404 Z= 0.215 Angle : 0.513 9.544 18206 Z= 0.269 Chirality : 0.038 0.131 2002 Planarity : 0.004 0.048 2292 Dihedral : 6.313 60.552 1894 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.74 % Allowed : 13.47 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.22), residues: 1604 helix: 2.58 (0.17), residues: 1000 sheet: -0.47 (0.41), residues: 174 loop : -1.01 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.003 0.001 HIS A 578 PHE 0.023 0.001 PHE A 397 TYR 0.009 0.001 TYR B 239 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 1.392 Fit side-chains REVERT: A 37 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6175 (mt) REVERT: A 161 ILE cc_start: 0.8552 (tp) cc_final: 0.8259 (tt) REVERT: A 229 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7330 (mtm-85) REVERT: A 651 HIS cc_start: 0.6794 (OUTLIER) cc_final: 0.5813 (p-80) REVERT: B 75 MET cc_start: 0.3282 (mpp) cc_final: 0.2881 (tpt) REVERT: B 183 ASN cc_start: 0.7301 (m-40) cc_final: 0.7064 (p0) REVERT: B 229 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7305 (mtm-85) REVERT: B 371 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7759 (mm-30) REVERT: B 552 TRP cc_start: 0.7691 (t-100) cc_final: 0.4803 (m-10) REVERT: B 651 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.5441 (p-80) REVERT: B 787 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7282 (tm-30) outliers start: 38 outliers final: 31 residues processed: 172 average time/residue: 0.2511 time to fit residues: 63.5690 Evaluate side-chains 174 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13404 Z= 0.200 Angle : 0.513 9.117 18206 Z= 0.270 Chirality : 0.038 0.128 2002 Planarity : 0.004 0.048 2292 Dihedral : 6.302 60.213 1894 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.67 % Allowed : 13.62 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.22), residues: 1604 helix: 2.56 (0.17), residues: 1000 sheet: -0.45 (0.41), residues: 174 loop : -1.00 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 PHE 0.025 0.001 PHE A 487 TYR 0.010 0.001 TYR B 492 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.475 Fit side-chains REVERT: A 37 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6170 (mt) REVERT: A 229 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7320 (mtm-85) REVERT: A 651 HIS cc_start: 0.6877 (OUTLIER) cc_final: 0.5988 (p-80) REVERT: B 75 MET cc_start: 0.3295 (mpp) cc_final: 0.2873 (tpt) REVERT: B 183 ASN cc_start: 0.7294 (m-40) cc_final: 0.7051 (p0) REVERT: B 229 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7294 (mtm-85) REVERT: B 371 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 552 TRP cc_start: 0.7735 (t-100) cc_final: 0.4790 (m-10) REVERT: B 651 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.5630 (p-80) REVERT: B 667 MET cc_start: 0.7857 (tpp) cc_final: 0.7565 (tpt) REVERT: B 787 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7260 (tm-30) outliers start: 37 outliers final: 31 residues processed: 170 average time/residue: 0.2424 time to fit residues: 61.6036 Evaluate side-chains 171 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13404 Z= 0.207 Angle : 0.524 10.456 18206 Z= 0.274 Chirality : 0.038 0.139 2002 Planarity : 0.004 0.048 2292 Dihedral : 6.274 60.032 1894 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.81 % Allowed : 13.69 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.22), residues: 1604 helix: 2.57 (0.17), residues: 1000 sheet: -0.47 (0.41), residues: 174 loop : -1.03 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 PHE 0.023 0.001 PHE A 397 TYR 0.009 0.001 TYR B 239 ARG 0.007 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.442 Fit side-chains REVERT: A 37 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6177 (mt) REVERT: A 229 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7261 (mtm-85) REVERT: A 651 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.5960 (p-80) REVERT: B 75 MET cc_start: 0.3407 (mpp) cc_final: 0.2944 (tpt) REVERT: B 183 ASN cc_start: 0.7252 (m-40) cc_final: 0.7012 (p0) REVERT: B 229 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7280 (mtm-85) REVERT: B 371 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7774 (mm-30) REVERT: B 552 TRP cc_start: 0.7741 (t-100) cc_final: 0.4787 (m-10) REVERT: B 651 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.5613 (p-80) REVERT: B 667 MET cc_start: 0.7865 (tpp) cc_final: 0.7535 (tpt) outliers start: 39 outliers final: 31 residues processed: 167 average time/residue: 0.2498 time to fit residues: 62.5502 Evaluate side-chains 169 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 111 optimal weight: 3.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.148948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115982 restraints weight = 15770.907| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.94 r_work: 0.3125 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13404 Z= 0.206 Angle : 0.519 9.838 18206 Z= 0.271 Chirality : 0.038 0.136 2002 Planarity : 0.004 0.048 2292 Dihedral : 6.262 59.799 1894 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.67 % Allowed : 13.62 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.22), residues: 1604 helix: 2.56 (0.17), residues: 1000 sheet: -0.45 (0.41), residues: 174 loop : -1.03 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 PHE 0.023 0.001 PHE A 397 TYR 0.009 0.001 TYR B 239 ARG 0.006 0.000 ARG B 199 =============================================================================== Job complete usr+sys time: 2622.74 seconds wall clock time: 49 minutes 22.32 seconds (2962.32 seconds total)