Starting phenix.real_space_refine on Sat Jul 26 02:22:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ehl_31142/07_2025/7ehl_31142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ehl_31142/07_2025/7ehl_31142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ehl_31142/07_2025/7ehl_31142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ehl_31142/07_2025/7ehl_31142.map" model { file = "/net/cci-nas-00/data/ceres_data/7ehl_31142/07_2025/7ehl_31142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ehl_31142/07_2025/7ehl_31142.cif" } resolution = 4.1 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 180 atoms to isotropic. 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 P 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5104 2.51 5 N 1400 2.21 5 O 1502 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-5711/modules/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 3936 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 14, 'TRANS': 548} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 3936 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 14, 'TRANS': 548} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 184 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' MG': 1, 'ANP': 1, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' MG': 1, 'ANP': 1, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.45, per 1000 atoms: 0.80 Number of scatterers: 8048 At special positions: 0 Unit cell: (100.386, 92.274, 136.89, 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) S 34 16.00 P 6 15.00 Mg 2 11.99 O 1502 8.00 N 1400 7.00 C 5104 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 70.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 144 through 182 Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 190 through 236 removed outlier: 3.826A pdb=" N LEU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.838A pdb=" N PHE A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 290 removed outlier: 3.915A pdb=" N ASP A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 331 Proline residue: A 303 - end of helix removed outlier: 4.081A pdb=" N MET A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.649A pdb=" N ASN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.680A pdb=" N VAL A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 403 removed outlier: 4.091A pdb=" N GLY A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 450 removed outlier: 4.132A pdb=" N VAL A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER A 418 " --> pdb=" O PHE A 414 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 542 through 550 Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.613A pdb=" N ARG A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 588 removed outlier: 3.729A pdb=" N TYR A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.590A pdb=" N THR A 595 " --> pdb=" O HIS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 627 removed outlier: 3.510A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.513A pdb=" N GLU A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 673 removed outlier: 3.518A pdb=" N THR A 672 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 removed outlier: 3.814A pdb=" N LYS A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 removed outlier: 3.654A pdb=" N GLU A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 144 through 182 Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 190 through 236 removed outlier: 3.826A pdb=" N LEU B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.838A pdb=" N PHE B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 290 removed outlier: 3.915A pdb=" N ASP B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 331 Proline residue: B 303 - end of helix removed outlier: 4.081A pdb=" N MET B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.649A pdb=" N ASN B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 347 removed outlier: 3.680A pdb=" N VAL B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 403 removed outlier: 4.091A pdb=" N GLY B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 450 removed outlier: 4.132A pdb=" N VAL B 416 " --> pdb=" O MET B 412 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA B 417 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 418 " --> pdb=" O PHE B 414 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 542 through 550 Processing helix chain 'B' and resid 564 through 570 removed outlier: 3.613A pdb=" N ARG B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 588 removed outlier: 3.729A pdb=" N TYR B 582 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 595 removed outlier: 3.590A pdb=" N THR B 595 " --> pdb=" O HIS B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 628 removed outlier: 3.718A pdb=" N ARG B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 658 removed outlier: 3.513A pdb=" N GLU B 647 " --> pdb=" O ASP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.518A pdb=" N THR B 672 " --> pdb=" O ARG B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 removed outlier: 3.814A pdb=" N LYS B 698 " --> pdb=" O GLU B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 711 removed outlier: 3.654A pdb=" N GLU B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 497 removed outlier: 3.694A pdb=" N VAL A 472 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 477 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 528 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 505 removed outlier: 6.440A pdb=" N LEU A 633 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE A 666 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 635 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 682 Processing sheet with id=AA4, first strand: chain 'B' and resid 496 through 497 removed outlier: 3.694A pdb=" N VAL B 472 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 477 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 528 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 502 through 505 removed outlier: 6.440A pdb=" N LEU B 633 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE B 666 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 635 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 678 through 682 602 hydrogen bonds defined for protein. 1794 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: 2.91 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2712 1.35 - 1.46: 1768 1.46 - 1.58: 3604 1.58 - 1.70: 30 1.70 - 1.81: 58 Bond restraints: 8172 Sorted by residual: bond pdb=" C5 CLR A 903 " pdb=" C6 CLR A 903 " ideal model delta sigma weight residual 1.332 1.558 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C5 CLR B1001 " pdb=" C6 CLR B1001 " ideal model delta sigma weight residual 1.332 1.558 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C5 CLR B1002 " pdb=" C6 CLR B1002 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C5 CLR A 901 " pdb=" C6 CLR A 901 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ANP B1003 " pdb=" C4' ANP B1003 " ideal model delta sigma weight residual 1.532 1.339 0.193 2.00e-02 2.50e+03 9.29e+01 ... (remaining 8167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 10821 2.48 - 4.97: 238 4.97 - 7.45: 67 7.45 - 9.94: 14 9.94 - 12.42: 18 Bond angle restraints: 11158 Sorted by residual: angle pdb=" C5 CLR A 903 " pdb=" C6 CLR A 903 " pdb=" C7 CLR A 903 " ideal model delta sigma weight residual 125.11 112.69 12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C5 CLR B1001 " pdb=" C6 CLR B1001 " pdb=" C7 CLR B1001 " ideal model delta sigma weight residual 125.11 112.69 12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C5 CLR B1002 " pdb=" C6 CLR B1002 " pdb=" C7 CLR B1002 " ideal model delta sigma weight residual 125.11 112.82 12.29 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C5 CLR A 901 " pdb=" C6 CLR A 901 " pdb=" C7 CLR A 901 " ideal model delta sigma weight residual 125.11 112.82 12.29 3.00e+00 1.11e-01 1.68e+01 angle pdb=" N ALA B 348 " pdb=" CA ALA B 348 " pdb=" C ALA B 348 " ideal model delta sigma weight residual 113.29 121.00 -7.71 2.00e+00 2.50e-01 1.48e+01 ... (remaining 11153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4535 17.38 - 34.75: 353 34.75 - 52.13: 91 52.13 - 69.51: 3 69.51 - 86.88: 18 Dihedral angle restraints: 5000 sinusoidal: 1832 harmonic: 3168 Sorted by residual: dihedral pdb=" CA PHE B 347 " pdb=" C PHE B 347 " pdb=" N ALA B 348 " pdb=" CA ALA B 348 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA PHE A 347 " pdb=" C PHE A 347 " pdb=" N ALA A 348 " pdb=" CA ALA A 348 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU B 580 " pdb=" CG GLU B 580 " pdb=" CD GLU B 580 " pdb=" OE1 GLU B 580 " ideal model delta sinusoidal sigma weight residual 0.00 82.62 -82.62 1 3.00e+01 1.11e-03 9.30e+00 ... (remaining 4997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1278 0.099 - 0.197: 62 0.197 - 0.296: 12 0.296 - 0.394: 2 0.394 - 0.492: 6 Chirality restraints: 1360 Sorted by residual: chirality pdb=" C13 CLR B1002 " pdb=" C12 CLR B1002 " pdb=" C14 CLR B1002 " pdb=" C17 CLR B1002 " both_signs ideal model delta sigma weight residual False -2.93 -2.44 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" C13 CLR A 901 " pdb=" C12 CLR A 901 " pdb=" C14 CLR A 901 " pdb=" C17 CLR A 901 " both_signs ideal model delta sigma weight residual False -2.93 -2.44 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" C13 CLR A 903 " pdb=" C12 CLR A 903 " pdb=" C14 CLR A 903 " pdb=" C17 CLR A 903 " both_signs ideal model delta sigma weight residual False -2.93 -2.45 -0.48 2.00e-01 2.50e+01 5.77e+00 ... (remaining 1357 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 619 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ARG A 619 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG A 619 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 620 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 347 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C PHE A 347 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE A 347 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 348 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 347 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C PHE B 347 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE B 347 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 348 " 0.010 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.98: 4081 2.98 - 3.62: 12767 3.62 - 4.26: 16186 4.26 - 4.90: 27147 Nonbonded interactions: 60204 Sorted by model distance: nonbonded pdb=" OD1 ASN B 568 " pdb=" NH2 ARG B 624 " model vdw 1.708 3.120 nonbonded pdb=" CG2 THR B 514 " pdb="MG MG B1004 " model vdw 1.970 2.590 nonbonded pdb=" CG2 THR A 514 " pdb="MG MG A 904 " model vdw 1.972 2.590 nonbonded pdb=" O2B ANP A 902 " pdb="MG MG A 904 " model vdw 2.062 2.170 nonbonded pdb=" O2B ANP B1003 " pdb="MG MG B1004 " model vdw 2.066 2.170 ... (remaining 60199 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 132 through 711 or resid 901 or resid 904)) selection = (chain 'B' and (resid 132 through 711 or resid 1001 or resid 1004)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.270 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.012 0.226 8172 Z= 0.592 Angle : 0.997 12.422 11158 Z= 0.457 Chirality : 0.059 0.492 1360 Planarity : 0.003 0.030 1418 Dihedral : 14.295 86.881 2964 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 2.19 (0.26), residues: 1102 helix: 2.50 (0.19), residues: 758 sheet: 0.76 (0.67), residues: 60 loop : -1.44 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 138 HIS 0.004 0.001 HIS B 668 PHE 0.015 0.001 PHE A 571 TYR 0.016 0.002 TYR B 202 ARG 0.004 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.10763 ( 602) hydrogen bonds : angle 4.74829 ( 1794) covalent geometry : bond 0.01155 ( 8172) covalent geometry : angle 0.99726 (11158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8160 (tp) cc_final: 0.7881 (tp) REVERT: A 223 MET cc_start: 0.8921 (tpt) cc_final: 0.8669 (tpp) REVERT: A 427 ASN cc_start: 0.9546 (m-40) cc_final: 0.9076 (m-40) REVERT: A 491 LYS cc_start: 0.8792 (tttt) cc_final: 0.8590 (tppt) REVERT: A 493 PHE cc_start: 0.8276 (t80) cc_final: 0.8033 (t80) REVERT: A 636 ASP cc_start: 0.8174 (t70) cc_final: 0.7922 (t70) REVERT: B 148 LEU cc_start: 0.8150 (tp) cc_final: 0.7929 (tp) REVERT: B 216 LEU cc_start: 0.8976 (tp) cc_final: 0.8575 (tp) REVERT: B 366 CYS cc_start: 0.8679 (m) cc_final: 0.8459 (m) REVERT: B 371 LEU cc_start: 0.9601 (tt) cc_final: 0.9299 (pp) REVERT: B 427 ASN cc_start: 0.9507 (m-40) cc_final: 0.8990 (m-40) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1568 time to fit residues: 53.1487 Evaluate side-chains 199 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095439 restraints weight = 25138.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098005 restraints weight = 14622.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099807 restraints weight = 9645.945| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8172 Z= 0.166 Angle : 0.594 7.463 11158 Z= 0.304 Chirality : 0.041 0.157 1360 Planarity : 0.003 0.036 1418 Dihedral : 7.234 81.345 1504 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.28 % Allowed : 3.51 % Favored : 96.21 % 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: 2.45 (0.26), residues: 1102 helix: 2.61 (0.19), residues: 766 sheet: 0.82 (0.65), residues: 62 loop : -1.18 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 138 HIS 0.004 0.001 HIS B 591 PHE 0.017 0.001 PHE A 553 TYR 0.011 0.002 TYR B 582 ARG 0.003 0.000 ARG B 619 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 602) hydrogen bonds : angle 3.97775 ( 1794) covalent geometry : bond 0.00334 ( 8172) covalent geometry : angle 0.59372 (11158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8261 (tp) cc_final: 0.7988 (tp) REVERT: A 216 LEU cc_start: 0.9123 (tp) cc_final: 0.8826 (tp) REVERT: A 355 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: A 427 ASN cc_start: 0.9589 (m-40) cc_final: 0.9135 (m-40) REVERT: A 553 PHE cc_start: 0.8598 (t80) cc_final: 0.8203 (t80) REVERT: A 655 ASP cc_start: 0.8713 (m-30) cc_final: 0.8384 (t70) REVERT: A 682 MET cc_start: 0.7436 (tpp) cc_final: 0.7183 (tpp) REVERT: B 216 LEU cc_start: 0.9070 (tp) cc_final: 0.8790 (tp) REVERT: B 356 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.8120 (mtm-85) REVERT: B 366 CYS cc_start: 0.8771 (m) cc_final: 0.8417 (m) REVERT: B 371 LEU cc_start: 0.9631 (tt) cc_final: 0.9369 (pp) REVERT: B 427 ASN cc_start: 0.9556 (m-40) cc_final: 0.9059 (m-40) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.1678 time to fit residues: 55.4365 Evaluate side-chains 187 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.101032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089107 restraints weight = 26739.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091554 restraints weight = 15364.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093255 restraints weight = 10056.029| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8172 Z= 0.298 Angle : 0.717 7.148 11158 Z= 0.389 Chirality : 0.043 0.162 1360 Planarity : 0.004 0.038 1418 Dihedral : 7.249 79.174 1504 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.42 % Allowed : 5.90 % Favored : 93.68 % 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: 1.68 (0.26), residues: 1102 helix: 1.97 (0.18), residues: 768 sheet: 0.65 (0.67), residues: 62 loop : -1.34 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 545 HIS 0.006 0.002 HIS B 591 PHE 0.023 0.003 PHE A 347 TYR 0.014 0.003 TYR B 202 ARG 0.005 0.001 ARG B 365 Details of bonding type rmsd hydrogen bonds : bond 0.05340 ( 602) hydrogen bonds : angle 4.42403 ( 1794) covalent geometry : bond 0.00578 ( 8172) covalent geometry : angle 0.71740 (11158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8928 (tp) cc_final: 0.8615 (tp) REVERT: A 148 LEU cc_start: 0.8353 (tp) cc_final: 0.8067 (tp) REVERT: A 199 LEU cc_start: 0.8637 (mt) cc_final: 0.8430 (mt) REVERT: A 216 LEU cc_start: 0.9212 (tp) cc_final: 0.8970 (tp) REVERT: A 223 MET cc_start: 0.8985 (tpt) cc_final: 0.8549 (tpt) REVERT: A 427 ASN cc_start: 0.9545 (m-40) cc_final: 0.9130 (m-40) REVERT: A 434 GLN cc_start: 0.8899 (mp10) cc_final: 0.8541 (mp10) REVERT: B 148 LEU cc_start: 0.8367 (tp) cc_final: 0.8146 (tp) REVERT: B 216 LEU cc_start: 0.9152 (tp) cc_final: 0.8919 (tp) REVERT: B 366 CYS cc_start: 0.8738 (m) cc_final: 0.8187 (m) REVERT: B 383 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8141 (t0) REVERT: B 422 GLN cc_start: 0.9078 (tt0) cc_final: 0.8329 (tp-100) REVERT: B 434 GLN cc_start: 0.8844 (mp10) cc_final: 0.8420 (mp10) REVERT: B 487 PHE cc_start: 0.6985 (t80) cc_final: 0.6758 (t80) REVERT: B 491 LYS cc_start: 0.9292 (tppt) cc_final: 0.8918 (mmtm) REVERT: B 537 ASP cc_start: 0.7533 (m-30) cc_final: 0.7285 (m-30) outliers start: 3 outliers final: 0 residues processed: 223 average time/residue: 0.1985 time to fit residues: 62.2209 Evaluate side-chains 188 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091078 restraints weight = 25858.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093599 restraints weight = 14611.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095343 restraints weight = 9470.434| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8172 Z= 0.184 Angle : 0.610 7.756 11158 Z= 0.325 Chirality : 0.041 0.153 1360 Planarity : 0.003 0.036 1418 Dihedral : 7.431 79.183 1504 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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 (0.26), residues: 1102 helix: 2.24 (0.19), residues: 758 sheet: 0.60 (0.67), residues: 62 loop : -1.09 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 138 HIS 0.004 0.001 HIS A 144 PHE 0.019 0.002 PHE A 347 TYR 0.013 0.002 TYR B 582 ARG 0.006 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.05220 ( 602) hydrogen bonds : angle 4.09197 ( 1794) covalent geometry : bond 0.00364 ( 8172) covalent geometry : angle 0.61047 (11158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8862 (tp) cc_final: 0.8524 (tp) REVERT: A 148 LEU cc_start: 0.8315 (tp) cc_final: 0.8021 (tp) REVERT: A 216 LEU cc_start: 0.9192 (tp) cc_final: 0.8943 (tp) REVERT: A 223 MET cc_start: 0.8916 (tpt) cc_final: 0.8476 (tpt) REVERT: A 367 ARG cc_start: 0.9052 (mmp80) cc_final: 0.8786 (mmp80) REVERT: A 383 ASN cc_start: 0.8376 (t0) cc_final: 0.8119 (t0) REVERT: A 427 ASN cc_start: 0.9540 (m-40) cc_final: 0.9117 (m-40) REVERT: A 434 GLN cc_start: 0.8771 (mp10) cc_final: 0.8517 (mp10) REVERT: B 148 LEU cc_start: 0.8305 (tp) cc_final: 0.8094 (tp) REVERT: B 223 MET cc_start: 0.8781 (tpt) cc_final: 0.8470 (tpt) REVERT: B 366 CYS cc_start: 0.8825 (m) cc_final: 0.8353 (m) REVERT: B 369 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7943 (mt-10) REVERT: B 422 GLN cc_start: 0.8981 (tt0) cc_final: 0.8215 (tp-100) REVERT: B 434 GLN cc_start: 0.8673 (mp10) cc_final: 0.8382 (mp10) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1750 time to fit residues: 54.9664 Evaluate side-chains 193 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.104624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093072 restraints weight = 25269.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095653 restraints weight = 14226.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097417 restraints weight = 9141.019| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8172 Z= 0.137 Angle : 0.587 7.790 11158 Z= 0.304 Chirality : 0.040 0.150 1360 Planarity : 0.003 0.035 1418 Dihedral : 7.283 76.846 1504 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 2.21 (0.26), residues: 1102 helix: 2.38 (0.19), residues: 758 sheet: 0.75 (0.69), residues: 62 loop : -1.00 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 138 HIS 0.005 0.001 HIS A 144 PHE 0.014 0.001 PHE A 553 TYR 0.016 0.002 TYR B 703 ARG 0.006 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 602) hydrogen bonds : angle 3.97216 ( 1794) covalent geometry : bond 0.00269 ( 8172) covalent geometry : angle 0.58713 (11158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8804 (tp) cc_final: 0.8437 (tp) REVERT: A 148 LEU cc_start: 0.8312 (tp) cc_final: 0.8048 (tp) REVERT: A 223 MET cc_start: 0.8924 (tpt) cc_final: 0.8637 (tpt) REVERT: A 266 PHE cc_start: 0.9139 (t80) cc_final: 0.8899 (t80) REVERT: A 367 ARG cc_start: 0.9052 (mmp80) cc_final: 0.8772 (mmp80) REVERT: A 383 ASN cc_start: 0.8440 (t0) cc_final: 0.8089 (t0) REVERT: A 427 ASN cc_start: 0.9603 (m-40) cc_final: 0.9123 (m-40) REVERT: B 223 MET cc_start: 0.8778 (tpt) cc_final: 0.8565 (tpt) REVERT: B 356 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8039 (mtm-85) REVERT: B 422 GLN cc_start: 0.8947 (tt0) cc_final: 0.8189 (tp40) REVERT: B 487 PHE cc_start: 0.7050 (t80) cc_final: 0.6728 (t80) REVERT: B 491 LYS cc_start: 0.9401 (tppt) cc_final: 0.9026 (mmtt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1721 time to fit residues: 54.3559 Evaluate side-chains 189 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.104634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092937 restraints weight = 25321.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095504 restraints weight = 14270.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097260 restraints weight = 9177.899| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8172 Z= 0.136 Angle : 0.570 7.612 11158 Z= 0.297 Chirality : 0.039 0.144 1360 Planarity : 0.003 0.035 1418 Dihedral : 7.163 75.270 1504 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.28 % Allowed : 1.83 % Favored : 97.89 % 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: 2.33 (0.26), residues: 1102 helix: 2.48 (0.19), residues: 758 sheet: 0.96 (0.69), residues: 62 loop : -1.04 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 138 HIS 0.004 0.001 HIS A 144 PHE 0.021 0.002 PHE B 266 TYR 0.015 0.002 TYR A 202 ARG 0.006 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 602) hydrogen bonds : angle 3.90214 ( 1794) covalent geometry : bond 0.00271 ( 8172) covalent geometry : angle 0.56995 (11158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8805 (tp) cc_final: 0.8412 (tp) REVERT: A 148 LEU cc_start: 0.8281 (tp) cc_final: 0.7996 (tp) REVERT: A 199 LEU cc_start: 0.8597 (mt) cc_final: 0.8387 (mt) REVERT: A 223 MET cc_start: 0.8945 (tpt) cc_final: 0.8526 (tpt) REVERT: A 266 PHE cc_start: 0.9131 (t80) cc_final: 0.8891 (t80) REVERT: A 367 ARG cc_start: 0.9108 (mmp80) cc_final: 0.8735 (mmp80) REVERT: A 383 ASN cc_start: 0.8390 (t0) cc_final: 0.8019 (t0) REVERT: A 427 ASN cc_start: 0.9584 (m-40) cc_final: 0.9123 (m-40) REVERT: A 557 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8864 (mt-10) REVERT: A 655 ASP cc_start: 0.8804 (m-30) cc_final: 0.8431 (t70) REVERT: B 223 MET cc_start: 0.8753 (tpt) cc_final: 0.8524 (tpt) REVERT: B 422 GLN cc_start: 0.8926 (tt0) cc_final: 0.8194 (tp40) REVERT: B 434 GLN cc_start: 0.8598 (mp10) cc_final: 0.8371 (mp10) REVERT: B 487 PHE cc_start: 0.7063 (t80) cc_final: 0.6730 (t80) outliers start: 2 outliers final: 1 residues processed: 225 average time/residue: 0.1771 time to fit residues: 55.1642 Evaluate side-chains 189 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 48 optimal weight: 0.0070 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096036 restraints weight = 25260.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098634 restraints weight = 14308.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100423 restraints weight = 9247.172| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8172 Z= 0.128 Angle : 0.584 7.953 11158 Z= 0.300 Chirality : 0.039 0.156 1360 Planarity : 0.003 0.033 1418 Dihedral : 7.014 73.685 1504 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 2.36 (0.26), residues: 1102 helix: 2.48 (0.19), residues: 758 sheet: 1.19 (0.68), residues: 62 loop : -1.01 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 545 HIS 0.003 0.001 HIS A 144 PHE 0.021 0.001 PHE B 266 TYR 0.015 0.002 TYR A 202 ARG 0.009 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 602) hydrogen bonds : angle 3.89461 ( 1794) covalent geometry : bond 0.00241 ( 8172) covalent geometry : angle 0.58364 (11158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8765 (tp) cc_final: 0.8395 (tp) REVERT: A 148 LEU cc_start: 0.8159 (tp) cc_final: 0.7881 (tp) REVERT: A 223 MET cc_start: 0.8976 (tpt) cc_final: 0.8674 (tpt) REVERT: A 266 PHE cc_start: 0.9106 (t80) cc_final: 0.8842 (t80) REVERT: A 367 ARG cc_start: 0.9115 (mmp80) cc_final: 0.8768 (mmp80) REVERT: A 427 ASN cc_start: 0.9583 (m-40) cc_final: 0.9123 (m-40) REVERT: A 655 ASP cc_start: 0.8691 (m-30) cc_final: 0.8366 (t70) REVERT: B 365 ARG cc_start: 0.7704 (ttt-90) cc_final: 0.7008 (ttt-90) REVERT: B 422 GLN cc_start: 0.8910 (tt0) cc_final: 0.8173 (tp40) REVERT: B 434 GLN cc_start: 0.8570 (mp10) cc_final: 0.8265 (mp10) REVERT: B 487 PHE cc_start: 0.7080 (t80) cc_final: 0.6775 (t80) REVERT: B 491 LYS cc_start: 0.9389 (tppt) cc_final: 0.9055 (mmtt) REVERT: B 655 ASP cc_start: 0.8457 (m-30) cc_final: 0.8102 (t70) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1700 time to fit residues: 53.3913 Evaluate side-chains 190 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.106490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.094692 restraints weight = 25447.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097301 restraints weight = 14470.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099021 restraints weight = 9311.694| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8172 Z= 0.136 Angle : 0.582 7.460 11158 Z= 0.304 Chirality : 0.040 0.152 1360 Planarity : 0.003 0.034 1418 Dihedral : 6.953 73.016 1504 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 2.47 (0.26), residues: 1102 helix: 2.58 (0.19), residues: 758 sheet: 1.18 (0.67), residues: 62 loop : -0.99 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 138 HIS 0.003 0.001 HIS A 144 PHE 0.019 0.001 PHE B 266 TYR 0.015 0.002 TYR A 202 ARG 0.008 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 602) hydrogen bonds : angle 3.86394 ( 1794) covalent geometry : bond 0.00273 ( 8172) covalent geometry : angle 0.58214 (11158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8791 (tp) cc_final: 0.8405 (tp) REVERT: A 148 LEU cc_start: 0.8162 (tp) cc_final: 0.7885 (tp) REVERT: A 223 MET cc_start: 0.8963 (tpt) cc_final: 0.8744 (tpt) REVERT: A 266 PHE cc_start: 0.9111 (t80) cc_final: 0.8858 (t80) REVERT: A 367 ARG cc_start: 0.9150 (mmp80) cc_final: 0.8725 (mmp80) REVERT: A 427 ASN cc_start: 0.9571 (m-40) cc_final: 0.9107 (m-40) REVERT: A 655 ASP cc_start: 0.8675 (m-30) cc_final: 0.8322 (t70) REVERT: B 136 LEU cc_start: 0.8988 (tp) cc_final: 0.8600 (tp) REVERT: B 148 LEU cc_start: 0.8210 (tp) cc_final: 0.7954 (tp) REVERT: B 223 MET cc_start: 0.8933 (tpt) cc_final: 0.8688 (tpt) REVERT: B 365 ARG cc_start: 0.7977 (ttt-90) cc_final: 0.7133 (ttt-90) REVERT: B 422 GLN cc_start: 0.8908 (tt0) cc_final: 0.8128 (tp40) REVERT: B 434 GLN cc_start: 0.8591 (mp10) cc_final: 0.8273 (mp10) REVERT: B 487 PHE cc_start: 0.7125 (t80) cc_final: 0.6873 (t80) REVERT: B 557 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8825 (pt0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2368 time to fit residues: 76.5136 Evaluate side-chains 187 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.094494 restraints weight = 25622.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097099 restraints weight = 14488.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098868 restraints weight = 9316.362| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8172 Z= 0.136 Angle : 0.585 7.566 11158 Z= 0.303 Chirality : 0.040 0.152 1360 Planarity : 0.003 0.039 1418 Dihedral : 6.901 73.617 1504 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 2.48 (0.26), residues: 1102 helix: 2.58 (0.19), residues: 756 sheet: 1.26 (0.67), residues: 62 loop : -0.97 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 138 HIS 0.003 0.001 HIS B 668 PHE 0.018 0.001 PHE B 266 TYR 0.016 0.002 TYR A 202 ARG 0.012 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 602) hydrogen bonds : angle 3.86175 ( 1794) covalent geometry : bond 0.00274 ( 8172) covalent geometry : angle 0.58530 (11158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8786 (tp) cc_final: 0.8407 (tp) REVERT: A 148 LEU cc_start: 0.8167 (tp) cc_final: 0.7886 (tp) REVERT: A 223 MET cc_start: 0.8977 (tpt) cc_final: 0.8709 (tpt) REVERT: A 266 PHE cc_start: 0.9140 (t80) cc_final: 0.8864 (t80) REVERT: A 356 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.7967 (mtm-85) REVERT: A 427 ASN cc_start: 0.9572 (m-40) cc_final: 0.9124 (m-40) REVERT: A 491 LYS cc_start: 0.9419 (tppt) cc_final: 0.9151 (mmtm) REVERT: A 655 ASP cc_start: 0.8676 (m-30) cc_final: 0.8326 (t70) REVERT: A 682 MET cc_start: 0.7845 (tpt) cc_final: 0.7580 (tpp) REVERT: B 136 LEU cc_start: 0.8987 (tp) cc_final: 0.8603 (tp) REVERT: B 148 LEU cc_start: 0.8193 (tp) cc_final: 0.7925 (tp) REVERT: B 365 ARG cc_start: 0.7680 (ttt-90) cc_final: 0.7458 (ttt180) REVERT: B 422 GLN cc_start: 0.8903 (tt0) cc_final: 0.8136 (tp40) REVERT: B 458 SER cc_start: 0.9025 (p) cc_final: 0.8738 (p) REVERT: B 487 PHE cc_start: 0.7086 (t80) cc_final: 0.6696 (t80) REVERT: B 557 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8442 (mm-30) REVERT: B 655 ASP cc_start: 0.8467 (m-30) cc_final: 0.8076 (t70) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1685 time to fit residues: 52.9193 Evaluate side-chains 183 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.105486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093810 restraints weight = 25488.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096363 restraints weight = 14505.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.098095 restraints weight = 9324.208| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8172 Z= 0.154 Angle : 0.604 7.150 11158 Z= 0.318 Chirality : 0.040 0.172 1360 Planarity : 0.003 0.047 1418 Dihedral : 6.816 73.863 1504 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 2.36 (0.26), residues: 1102 helix: 2.49 (0.19), residues: 756 sheet: 1.28 (0.66), residues: 62 loop : -1.03 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 688 HIS 0.004 0.001 HIS B 668 PHE 0.017 0.002 PHE B 266 TYR 0.016 0.002 TYR A 202 ARG 0.011 0.001 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 602) hydrogen bonds : angle 3.95625 ( 1794) covalent geometry : bond 0.00309 ( 8172) covalent geometry : angle 0.60407 (11158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8817 (tp) cc_final: 0.8416 (tp) REVERT: A 148 LEU cc_start: 0.8176 (tp) cc_final: 0.7877 (tp) REVERT: A 199 LEU cc_start: 0.8573 (mt) cc_final: 0.8367 (mt) REVERT: A 223 MET cc_start: 0.8980 (tpt) cc_final: 0.8696 (tpt) REVERT: A 266 PHE cc_start: 0.9148 (t80) cc_final: 0.8873 (t80) REVERT: A 491 LYS cc_start: 0.9471 (tppt) cc_final: 0.9210 (mmtm) REVERT: A 655 ASP cc_start: 0.8650 (m-30) cc_final: 0.8291 (t70) REVERT: B 148 LEU cc_start: 0.8166 (tp) cc_final: 0.7900 (tp) REVERT: B 216 LEU cc_start: 0.9113 (tp) cc_final: 0.8729 (tp) REVERT: B 223 MET cc_start: 0.8739 (tpt) cc_final: 0.8501 (tpt) REVERT: B 422 GLN cc_start: 0.8904 (tt0) cc_final: 0.8146 (tp40) REVERT: B 434 GLN cc_start: 0.8664 (mp10) cc_final: 0.8439 (mp10) REVERT: B 458 SER cc_start: 0.9063 (p) cc_final: 0.8782 (p) REVERT: B 491 LYS cc_start: 0.9370 (tppt) cc_final: 0.9100 (mmtm) REVERT: B 557 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8396 (mm-30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1612 time to fit residues: 50.4156 Evaluate side-chains 186 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095201 restraints weight = 25471.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097763 restraints weight = 14502.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099504 restraints weight = 9362.760| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8172 Z= 0.135 Angle : 0.621 8.753 11158 Z= 0.324 Chirality : 0.041 0.186 1360 Planarity : 0.003 0.034 1418 Dihedral : 6.789 75.469 1504 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 2.37 (0.26), residues: 1102 helix: 2.48 (0.19), residues: 756 sheet: 1.33 (0.67), residues: 62 loop : -0.96 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 688 HIS 0.003 0.001 HIS B 668 PHE 0.017 0.001 PHE B 266 TYR 0.017 0.002 TYR B 357 ARG 0.010 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 602) hydrogen bonds : angle 3.98551 ( 1794) covalent geometry : bond 0.00271 ( 8172) covalent geometry : angle 0.62080 (11158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2602.92 seconds wall clock time: 46 minutes 29.65 seconds (2789.65 seconds total)