Starting phenix.real_space_refine on Thu Jun 12 02:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hob_34924/06_2025/8hob_34924_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hob_34924/06_2025/8hob_34924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hob_34924/06_2025/8hob_34924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hob_34924/06_2025/8hob_34924.map" model { file = "/net/cci-nas-00/data/ceres_data/8hob_34924/06_2025/8hob_34924_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hob_34924/06_2025/8hob_34924_neut.cif" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 36 5.16 5 C 8402 2.51 5 N 2190 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13449 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "B" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Time building chain proxies: 8.64, per 1000 atoms: 0.64 Number of scatterers: 13449 At special positions: 0 Unit cell: (145.25, 95.45, 97.11, 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 36 16.00 O 2821 8.00 N 2190 7.00 C 8402 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 25 sheets defined 33.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.811A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 331 through 344 Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.710A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.697A pdb=" N THR A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 433 removed outlier: 3.978A pdb=" N TRP A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.788A pdb=" N ILE A 437 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.989A pdb=" N VAL A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.951A pdb=" N LYS A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 557 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.719A pdb=" N GLY A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.499A pdb=" N ILE A 638 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 641 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 4.067A pdb=" N TRP A 658 " --> pdb=" O HIS A 654 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.768A pdb=" N ILE A 679 " --> pdb=" O TYR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.557A pdb=" N TRP A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.857A pdb=" N PHE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 331 through 344 Processing helix chain 'B' and resid 360 through 371 removed outlier: 3.710A pdb=" N LEU B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.693A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 433 removed outlier: 4.007A pdb=" N TRP B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.744A pdb=" N ILE B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.991A pdb=" N VAL B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 4.012A pdb=" N LYS B 524 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 557 Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.714A pdb=" N GLY B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 615 Processing helix chain 'B' and resid 635 through 641 removed outlier: 4.514A pdb=" N ILE B 638 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B 641 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 4.070A pdb=" N TRP B 658 " --> pdb=" O HIS B 654 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.763A pdb=" N ILE B 679 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.556A pdb=" N TRP B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.652A pdb=" N SER A 95 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.553A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.553A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 208 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 244 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE A 206 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.832A pdb=" N VAL A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 444 removed outlier: 3.970A pdb=" N PHE A 444 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYS A 450 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AB2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 702 removed outlier: 6.632A pdb=" N ALA A 699 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER A 716 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 739 removed outlier: 3.879A pdb=" N LEU A 743 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 3.649A pdb=" N SER B 95 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.743A pdb=" N HIS B 245 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER B 208 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 244 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 206 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.848A pdb=" N VAL B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 316 through 319 Processing sheet with id=AC1, first strand: chain 'B' and resid 358 through 359 Processing sheet with id=AC2, first strand: chain 'B' and resid 441 through 444 removed outlier: 3.949A pdb=" N PHE B 444 " --> pdb=" O LYS B 450 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LYS B 450 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AC4, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AC5, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AC6, first strand: chain 'B' and resid 699 through 702 removed outlier: 6.631A pdb=" N ALA B 699 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER B 716 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 739 removed outlier: 3.891A pdb=" N LEU B 743 " --> pdb=" O LEU B 796 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1623 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: 5.79 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 4 0.99 - 1.20: 4 1.20 - 1.40: 5863 1.40 - 1.61: 7523 1.61 - 1.81: 68 Bond restraints: 13462 Sorted by residual: bond pdb=" C GLN B 166 " pdb=" O GLN B 166 " ideal model delta sigma weight residual 1.236 0.791 0.445 1.18e-02 7.18e+03 1.42e+03 bond pdb=" C ASN B 168 " pdb=" O ASN B 168 " ideal model delta sigma weight residual 1.236 0.822 0.414 1.28e-02 6.10e+03 1.04e+03 bond pdb=" C ARG B 167 " pdb=" O ARG B 167 " ideal model delta sigma weight residual 1.235 0.933 0.301 1.03e-02 9.43e+03 8.56e+02 bond pdb=" C PHE B 165 " pdb=" O PHE B 165 " ideal model delta sigma weight residual 1.236 0.904 0.332 1.26e-02 6.30e+03 6.96e+02 bond pdb=" CA GLN B 166 " pdb=" C GLN B 166 " ideal model delta sigma weight residual 1.523 1.290 0.233 1.35e-02 5.49e+03 2.98e+02 ... (remaining 13457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.42: 18181 6.42 - 12.85: 14 12.85 - 19.27: 7 19.27 - 25.69: 2 25.69 - 32.12: 2 Bond angle restraints: 18206 Sorted by residual: angle pdb=" N GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta sigma weight residual 110.06 80.76 29.30 1.50e+00 4.44e-01 3.82e+02 angle pdb=" C GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta sigma weight residual 110.68 142.80 -32.12 1.70e+00 3.46e-01 3.57e+02 angle pdb=" CA ASN B 168 " pdb=" CB ASN B 168 " pdb=" CG ASN B 168 " ideal model delta sigma weight residual 112.60 129.82 -17.22 1.00e+00 1.00e+00 2.97e+02 angle pdb=" CA PHE B 165 " pdb=" CB PHE B 165 " pdb=" CG PHE B 165 " ideal model delta sigma weight residual 113.80 128.11 -14.31 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C ASN B 164 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " ideal model delta sigma weight residual 120.31 142.04 -21.73 1.52e+00 4.33e-01 2.04e+02 ... (remaining 18201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6862 17.93 - 35.86: 730 35.86 - 53.78: 229 53.78 - 71.71: 50 71.71 - 89.64: 21 Dihedral angle restraints: 7892 sinusoidal: 3192 harmonic: 4700 Sorted by residual: dihedral pdb=" C GLN B 166 " pdb=" N GLN B 166 " pdb=" CA GLN B 166 " pdb=" CB GLN B 166 " ideal model delta harmonic sigma weight residual -122.60 -148.42 25.82 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" C ARG B 167 " pdb=" N ARG B 167 " pdb=" CA ARG B 167 " pdb=" CB ARG B 167 " ideal model delta harmonic sigma weight residual -122.60 -144.26 21.66 0 2.50e+00 1.60e-01 7.51e+01 dihedral pdb=" C PHE B 165 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " pdb=" CB PHE B 165 " ideal model delta harmonic sigma weight residual -122.60 -143.69 21.09 0 2.50e+00 1.60e-01 7.12e+01 ... (remaining 7889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 1854 0.290 - 0.580: 0 0.580 - 0.870: 1 0.870 - 1.160: 2 1.160 - 1.450: 1 Chirality restraints: 1858 Sorted by residual: chirality pdb=" CA GLN B 166 " pdb=" N GLN B 166 " pdb=" C GLN B 166 " pdb=" CB GLN B 166 " both_signs ideal model delta sigma weight residual False 2.51 1.06 1.45 2.00e-01 2.50e+01 5.26e+01 chirality pdb=" CA PHE B 165 " pdb=" N PHE B 165 " pdb=" C PHE B 165 " pdb=" CB PHE B 165 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CA ARG B 167 " pdb=" N ARG B 167 " pdb=" C ARG B 167 " pdb=" CB ARG B 167 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 1855 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 168 " 0.030 2.00e-02 2.50e+03 7.53e-02 5.67e+01 pdb=" C ASN B 168 " -0.129 2.00e-02 2.50e+03 pdb=" O ASN B 168 " 0.061 2.00e-02 2.50e+03 pdb=" N PHE B 169 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 165 " 0.019 2.00e-02 2.50e+03 4.30e-02 1.84e+01 pdb=" C PHE B 165 " -0.074 2.00e-02 2.50e+03 pdb=" O PHE B 165 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN B 166 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 165 " 0.004 2.00e-02 2.50e+03 2.88e-02 1.45e+01 pdb=" CG PHE B 165 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 165 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 165 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE B 165 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B 165 " 0.040 2.00e-02 2.50e+03 pdb=" CZ PHE B 165 " -0.033 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2296 2.76 - 3.30: 12140 3.30 - 3.83: 25906 3.83 - 4.37: 32785 4.37 - 4.90: 50930 Nonbonded interactions: 124057 Sorted by model distance: nonbonded pdb=" OD2 ASP A 706 " pdb=" O HOH A 901 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 31 " pdb=" OE2 GLU B 32 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP A 209 " pdb=" O HOH A 902 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP B 209 " pdb=" O HOH B 901 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 160 " pdb=" O HOH A 903 " model vdw 2.268 3.040 ... (remaining 124052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.360 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.008 0.445 13462 Z= 0.649 Angle : 0.753 32.118 18206 Z= 0.482 Chirality : 0.066 1.450 1858 Planarity : 0.005 0.083 2372 Dihedral : 17.238 89.641 4916 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.23 % Allowed : 17.05 % Favored : 81.72 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1618 helix: 1.14 (0.24), residues: 482 sheet: 1.27 (0.30), residues: 282 loop : -0.19 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.003 0.001 HIS A 245 PHE 0.040 0.002 PHE B 165 TYR 0.014 0.001 TYR A 526 ARG 0.054 0.001 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.11933 ( 577) hydrogen bonds : angle 6.20292 ( 1623) covalent geometry : bond 0.00845 (13462) covalent geometry : angle 0.75311 (18206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.550 Fit side-chains REVERT: A 258 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 167 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7336 (ttt180) outliers start: 17 outliers final: 14 residues processed: 147 average time/residue: 1.7964 time to fit residues: 282.5948 Evaluate side-chains 143 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 chunk 41 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.085614 restraints weight = 14305.761| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.27 r_work: 0.2887 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13462 Z= 0.196 Angle : 0.582 6.428 18206 Z= 0.326 Chirality : 0.048 0.180 1858 Planarity : 0.004 0.039 2372 Dihedral : 7.412 80.168 1827 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.66 % Allowed : 16.62 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1618 helix: 1.13 (0.23), residues: 478 sheet: 1.27 (0.30), residues: 282 loop : -0.24 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.006 0.001 HIS B 545 PHE 0.022 0.002 PHE B 370 TYR 0.018 0.002 TYR A 526 ARG 0.004 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 577) hydrogen bonds : angle 5.81793 ( 1623) covalent geometry : bond 0.00451 (13462) covalent geometry : angle 0.58204 (18206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.582 Fit side-chains REVERT: A 91 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8301 (mtt180) REVERT: A 160 ASP cc_start: 0.8649 (t70) cc_final: 0.8442 (t70) REVERT: A 258 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: A 538 GLU cc_start: 0.7990 (mp0) cc_final: 0.7705 (mp0) REVERT: B 258 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8391 (mt-10) outliers start: 23 outliers final: 13 residues processed: 147 average time/residue: 1.8579 time to fit residues: 292.0693 Evaluate side-chains 140 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 47 optimal weight: 0.0270 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.100262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.088196 restraints weight = 14593.409| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.26 r_work: 0.2915 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13462 Z= 0.135 Angle : 0.523 5.568 18206 Z= 0.294 Chirality : 0.046 0.142 1858 Planarity : 0.004 0.040 2372 Dihedral : 6.749 75.673 1813 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.02 % Allowed : 16.33 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1618 helix: 1.26 (0.24), residues: 476 sheet: 1.20 (0.30), residues: 284 loop : -0.20 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 332 HIS 0.003 0.001 HIS B 545 PHE 0.021 0.002 PHE B 370 TYR 0.014 0.001 TYR A 14 ARG 0.007 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 577) hydrogen bonds : angle 5.66365 ( 1623) covalent geometry : bond 0.00296 (13462) covalent geometry : angle 0.52251 (18206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.497 Fit side-chains REVERT: A 160 ASP cc_start: 0.8647 (t70) cc_final: 0.8439 (t70) REVERT: A 258 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8326 (mt-10) REVERT: A 538 GLU cc_start: 0.7952 (mp0) cc_final: 0.7642 (mp0) REVERT: A 600 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: B 138 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: B 258 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: B 538 GLU cc_start: 0.7940 (mp0) cc_final: 0.7719 (mp0) outliers start: 28 outliers final: 14 residues processed: 149 average time/residue: 1.9704 time to fit residues: 313.5183 Evaluate side-chains 145 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 83 optimal weight: 0.0470 chunk 141 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 131 optimal weight: 0.0040 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0096 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.099284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.087068 restraints weight = 14302.753| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.27 r_work: 0.2912 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13462 Z= 0.141 Angle : 0.527 5.462 18206 Z= 0.296 Chirality : 0.046 0.143 1858 Planarity : 0.004 0.042 2372 Dihedral : 6.647 73.570 1811 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.24 % Allowed : 15.75 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1618 helix: 1.28 (0.24), residues: 478 sheet: 1.37 (0.30), residues: 272 loop : -0.24 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 332 HIS 0.004 0.001 HIS B 545 PHE 0.021 0.002 PHE B 370 TYR 0.014 0.001 TYR A 14 ARG 0.008 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 577) hydrogen bonds : angle 5.63114 ( 1623) covalent geometry : bond 0.00315 (13462) covalent geometry : angle 0.52697 (18206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.760 Fit side-chains REVERT: A 91 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8284 (mtt180) REVERT: A 160 ASP cc_start: 0.8628 (t70) cc_final: 0.8389 (t70) REVERT: A 258 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: A 538 GLU cc_start: 0.7930 (mp0) cc_final: 0.7668 (mp0) REVERT: A 600 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: B 138 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: B 258 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: B 538 GLU cc_start: 0.7935 (mp0) cc_final: 0.7707 (mp0) outliers start: 31 outliers final: 17 residues processed: 149 average time/residue: 1.9373 time to fit residues: 307.9794 Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 109 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 161 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.099482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.087213 restraints weight = 14432.446| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.27 r_work: 0.2915 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13462 Z= 0.140 Angle : 0.525 5.389 18206 Z= 0.295 Chirality : 0.046 0.142 1858 Planarity : 0.004 0.042 2372 Dihedral : 6.624 71.675 1811 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.10 % Allowed : 15.75 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1618 helix: 1.28 (0.24), residues: 476 sheet: 1.37 (0.30), residues: 272 loop : -0.25 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 332 HIS 0.003 0.001 HIS B 545 PHE 0.020 0.002 PHE B 370 TYR 0.014 0.001 TYR A 14 ARG 0.008 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 577) hydrogen bonds : angle 5.60945 ( 1623) covalent geometry : bond 0.00312 (13462) covalent geometry : angle 0.52517 (18206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.639 Fit side-chains REVERT: A 91 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8289 (mtt180) REVERT: A 160 ASP cc_start: 0.8601 (t70) cc_final: 0.8358 (t70) REVERT: A 258 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: A 380 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: A 538 GLU cc_start: 0.7930 (mp0) cc_final: 0.7670 (mp0) REVERT: A 600 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: B 138 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: B 258 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: B 380 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: B 538 GLU cc_start: 0.7932 (mp0) cc_final: 0.7704 (mp0) outliers start: 29 outliers final: 18 residues processed: 143 average time/residue: 2.0297 time to fit residues: 310.5194 Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 133 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 160 optimal weight: 0.0770 chunk 137 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.085575 restraints weight = 14504.458| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.28 r_work: 0.2887 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13462 Z= 0.188 Angle : 0.574 5.765 18206 Z= 0.321 Chirality : 0.048 0.143 1858 Planarity : 0.004 0.043 2372 Dihedral : 6.786 73.425 1811 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.17 % Allowed : 15.82 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1618 helix: 1.14 (0.23), residues: 480 sheet: 1.29 (0.29), residues: 282 loop : -0.29 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.005 0.001 HIS B 545 PHE 0.020 0.002 PHE B 370 TYR 0.017 0.002 TYR B 526 ARG 0.008 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 577) hydrogen bonds : angle 5.72534 ( 1623) covalent geometry : bond 0.00433 (13462) covalent geometry : angle 0.57378 (18206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.801 Fit side-chains REVERT: A 91 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8317 (mtt180) REVERT: A 160 ASP cc_start: 0.8652 (t70) cc_final: 0.8368 (t70) REVERT: A 258 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: A 380 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: A 538 GLU cc_start: 0.7987 (mp0) cc_final: 0.7702 (mp0) REVERT: A 600 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: B 138 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: B 258 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: B 380 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: B 538 GLU cc_start: 0.8010 (mp0) cc_final: 0.7760 (mp0) outliers start: 30 outliers final: 17 residues processed: 146 average time/residue: 2.6658 time to fit residues: 415.8065 Evaluate side-chains 148 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 148 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.099301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087061 restraints weight = 14369.974| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.27 r_work: 0.2913 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13462 Z= 0.138 Angle : 0.529 5.489 18206 Z= 0.296 Chirality : 0.046 0.142 1858 Planarity : 0.004 0.043 2372 Dihedral : 6.651 70.408 1811 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.88 % Allowed : 16.11 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1618 helix: 1.28 (0.24), residues: 476 sheet: 1.35 (0.30), residues: 272 loop : -0.24 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 332 HIS 0.003 0.001 HIS B 245 PHE 0.020 0.002 PHE B 370 TYR 0.014 0.001 TYR A 14 ARG 0.008 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 577) hydrogen bonds : angle 5.61763 ( 1623) covalent geometry : bond 0.00306 (13462) covalent geometry : angle 0.52876 (18206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 4.004 Fit side-chains REVERT: A 91 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8295 (mtt180) REVERT: A 160 ASP cc_start: 0.8574 (t70) cc_final: 0.8314 (t70) REVERT: A 380 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 538 GLU cc_start: 0.7897 (mp0) cc_final: 0.7633 (mp0) REVERT: A 600 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: B 138 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: B 258 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: B 380 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: B 538 GLU cc_start: 0.7924 (mp0) cc_final: 0.7705 (mp0) outliers start: 26 outliers final: 18 residues processed: 148 average time/residue: 3.1965 time to fit residues: 509.9671 Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.085176 restraints weight = 14553.071| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.28 r_work: 0.2879 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13462 Z= 0.206 Angle : 0.593 6.415 18206 Z= 0.331 Chirality : 0.049 0.146 1858 Planarity : 0.004 0.044 2372 Dihedral : 6.480 57.863 1808 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.95 % Allowed : 16.11 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1618 helix: 1.09 (0.23), residues: 480 sheet: 1.14 (0.29), residues: 294 loop : -0.26 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.005 0.001 HIS B 545 PHE 0.021 0.002 PHE B 370 TYR 0.018 0.002 TYR A 526 ARG 0.007 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.05279 ( 577) hydrogen bonds : angle 5.75507 ( 1623) covalent geometry : bond 0.00478 (13462) covalent geometry : angle 0.59285 (18206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.952 Fit side-chains REVERT: A 91 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8319 (mtt180) REVERT: A 160 ASP cc_start: 0.8662 (t70) cc_final: 0.8381 (t70) REVERT: A 258 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: A 380 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: A 538 GLU cc_start: 0.7924 (mp0) cc_final: 0.7662 (mp0) REVERT: A 600 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: B 138 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: B 258 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: B 380 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: B 538 GLU cc_start: 0.8010 (mp0) cc_final: 0.7733 (mp0) outliers start: 27 outliers final: 18 residues processed: 147 average time/residue: 2.4028 time to fit residues: 378.0474 Evaluate side-chains 152 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 64 optimal weight: 0.0060 chunk 61 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089199 restraints weight = 14318.999| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.26 r_work: 0.2948 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13462 Z= 0.105 Angle : 0.494 5.231 18206 Z= 0.277 Chirality : 0.044 0.141 1858 Planarity : 0.004 0.042 2372 Dihedral : 6.116 58.003 1808 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.59 % Allowed : 16.40 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1618 helix: 1.37 (0.24), residues: 478 sheet: 1.18 (0.30), residues: 284 loop : -0.17 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 332 HIS 0.003 0.001 HIS B 245 PHE 0.020 0.001 PHE A 370 TYR 0.011 0.001 TYR A 14 ARG 0.008 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 577) hydrogen bonds : angle 5.48303 ( 1623) covalent geometry : bond 0.00219 (13462) covalent geometry : angle 0.49395 (18206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.618 Fit side-chains REVERT: A 91 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8271 (mtt180) REVERT: A 160 ASP cc_start: 0.8513 (t70) cc_final: 0.8240 (t70) REVERT: A 380 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: A 538 GLU cc_start: 0.7873 (mp0) cc_final: 0.7652 (mp0) REVERT: A 600 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 138 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: B 380 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7569 (tt0) outliers start: 22 outliers final: 14 residues processed: 144 average time/residue: 1.8818 time to fit residues: 289.4353 Evaluate side-chains 145 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.084819 restraints weight = 14411.508| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.27 r_work: 0.2875 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13462 Z= 0.232 Angle : 0.620 7.027 18206 Z= 0.345 Chirality : 0.050 0.147 1858 Planarity : 0.005 0.044 2372 Dihedral : 6.495 56.825 1808 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.45 % Allowed : 16.69 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1618 helix: 1.06 (0.23), residues: 480 sheet: 1.16 (0.29), residues: 294 loop : -0.26 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.005 0.001 HIS B 545 PHE 0.020 0.003 PHE B 370 TYR 0.021 0.002 TYR A 526 ARG 0.008 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.05505 ( 577) hydrogen bonds : angle 5.78079 ( 1623) covalent geometry : bond 0.00541 (13462) covalent geometry : angle 0.62015 (18206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.528 Fit side-chains REVERT: A 91 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8327 (mtt180) REVERT: A 160 ASP cc_start: 0.8682 (t70) cc_final: 0.8391 (t70) REVERT: A 258 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: A 380 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 537 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7252 (mp0) REVERT: A 538 GLU cc_start: 0.7987 (mp0) cc_final: 0.7718 (mp0) REVERT: A 600 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: B 138 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8316 (mt-10) REVERT: B 380 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7682 (tt0) outliers start: 20 outliers final: 12 residues processed: 143 average time/residue: 1.9011 time to fit residues: 292.6315 Evaluate side-chains 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 78 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.084858 restraints weight = 14350.718| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.27 r_work: 0.2851 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13462 Z= 0.153 Angle : 0.554 5.624 18206 Z= 0.310 Chirality : 0.047 0.143 1858 Planarity : 0.004 0.044 2372 Dihedral : 6.336 57.825 1807 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.45 % Allowed : 16.62 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1618 helix: 1.18 (0.24), residues: 474 sheet: 1.12 (0.29), residues: 294 loop : -0.22 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.003 0.001 HIS B 545 PHE 0.020 0.002 PHE A 370 TYR 0.014 0.002 TYR B 526 ARG 0.009 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 577) hydrogen bonds : angle 5.67132 ( 1623) covalent geometry : bond 0.00345 (13462) covalent geometry : angle 0.55403 (18206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11686.64 seconds wall clock time: 209 minutes 3.54 seconds (12543.54 seconds total)