Starting phenix.real_space_refine on Sun Dec 29 13:57:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7myo_24082/12_2024/7myo_24082.cif Found real_map, /net/cci-nas-00/data/ceres_data/7myo_24082/12_2024/7myo_24082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7myo_24082/12_2024/7myo_24082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7myo_24082/12_2024/7myo_24082.map" model { file = "/net/cci-nas-00/data/ceres_data/7myo_24082/12_2024/7myo_24082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7myo_24082/12_2024/7myo_24082.cif" } resolution = 2.92 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: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 6763 2.51 5 N 1848 2.21 5 O 1943 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10634 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2412 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 281} Chain: "A" Number of atoms: 8192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 992, 8107 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 992, 8107 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8193 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'1LT': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AARG A 617 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 617 " occ=0.50 residue: pdb=" N ALYS A 621 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 621 " occ=0.50 residue: pdb=" N AARG A 662 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 662 " occ=0.50 residue: pdb=" N AARG A 899 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 899 " occ=0.50 residue: pdb=" N AARG A 951 " occ=0.63 ... (20 atoms not shown) pdb=" NH2BARG A 951 " occ=0.37 residue: pdb=" N AVAL A 952 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 952 " occ=0.37 residue: pdb=" N APRO A 953 " occ=0.63 ... (12 atoms not shown) pdb=" CD BPRO A 953 " occ=0.37 residue: pdb=" N APHE A 954 " occ=0.63 ... (20 atoms not shown) pdb=" CZ BPHE A 954 " occ=0.37 residue: pdb=" N AVAL A 955 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.37 Time building chain proxies: 9.68, per 1000 atoms: 0.91 Number of scatterers: 10634 At special positions: 0 Unit cell: (89.87, 108.68, 135.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 F 3 9.00 O 1943 8.00 N 1848 7.00 C 6763 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: 2.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 50.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.091A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 441 through 506 removed outlier: 3.595A pdb=" N VAL B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.799A pdb=" N PHE B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 588 removed outlier: 3.927A pdb=" N LEU B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 593 through 599 removed outlier: 3.915A pdb=" N TRP B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 56 removed outlier: 3.605A pdb=" N HIS A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.815A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.990A pdb=" N PHE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 3.541A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.657A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.785A pdb=" N VAL A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.690A pdb=" N VAL A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.863A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.824A pdb=" N LYS A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.620A pdb=" N ALA A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 removed outlier: 4.119A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 642 removed outlier: 3.902A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 641 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 642 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 721 removed outlier: 3.807A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 787 through 793 removed outlier: 4.438A pdb=" N GLU A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 Processing helix chain 'A' and resid 857 through 867 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 911 removed outlier: 4.451A pdb=" N VAL A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.521A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 965 " --> pdb=" O LEU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 993 removed outlier: 4.092A pdb=" N GLU A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.696A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1026 Processing helix chain 'A' and resid 1031 through 1045 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AA2, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36 removed outlier: 3.615A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 101 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 25 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 212 removed outlier: 8.429A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 253 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.393A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.516A pdb=" N VAL A 409 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.430A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 752 through 753 removed outlier: 5.885A pdb=" N HIS A 759 " --> pdb=" O SER A 753 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AB1, first strand: chain 'A' and resid 854 through 856 499 hydrogen bonds defined for protein. 1437 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: 3.40 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1774 1.32 - 1.44: 2816 1.44 - 1.56: 6146 1.56 - 1.69: 2 1.69 - 1.81: 121 Bond restraints: 10859 Sorted by residual: bond pdb=" C3 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.391 1.485 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.458 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C3 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.348 1.435 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.445 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C7 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.444 1.520 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 10854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 14279 2.57 - 5.14: 306 5.14 - 7.71: 57 7.71 - 10.28: 5 10.28 - 12.86: 4 Bond angle restraints: 14651 Sorted by residual: angle pdb=" N ASP A1017 " pdb=" CA ASP A1017 " pdb=" C ASP A1017 " ideal model delta sigma weight residual 114.31 108.20 6.11 1.29e+00 6.01e-01 2.25e+01 angle pdb=" C ASP A 939 " pdb=" N HIS A 940 " pdb=" CA HIS A 940 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" N GLU B 537 " pdb=" CA GLU B 537 " pdb=" CB GLU B 537 " ideal model delta sigma weight residual 110.30 117.00 -6.70 1.54e+00 4.22e-01 1.90e+01 angle pdb=" CB MET A1040 " pdb=" CG MET A1040 " pdb=" SD MET A1040 " ideal model delta sigma weight residual 112.70 125.56 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CG1 ILE A 211 " pdb=" CB ILE A 211 " pdb=" CG2 ILE A 211 " ideal model delta sigma weight residual 110.70 99.90 10.80 3.00e+00 1.11e-01 1.30e+01 ... (remaining 14646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5886 17.47 - 34.95: 618 34.95 - 52.42: 113 52.42 - 69.89: 32 69.89 - 87.36: 13 Dihedral angle restraints: 6662 sinusoidal: 2859 harmonic: 3803 Sorted by residual: dihedral pdb=" CA LEU A 209 " pdb=" C LEU A 209 " pdb=" N LYS A 210 " pdb=" CA LYS A 210 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE B 512 " pdb=" C PHE B 512 " pdb=" N LYS B 513 " pdb=" CA LYS B 513 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 262 " pdb=" C LEU A 262 " pdb=" N GLU A 263 " pdb=" CA GLU A 263 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1062 0.044 - 0.088: 374 0.088 - 0.132: 117 0.132 - 0.175: 19 0.175 - 0.219: 9 Chirality restraints: 1581 Sorted by residual: chirality pdb=" CB ILE A 921 " pdb=" CA ILE A 921 " pdb=" CG1 ILE A 921 " pdb=" CG2 ILE A 921 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN A 202 " pdb=" N ASN A 202 " pdb=" C ASN A 202 " pdb=" CB ASN A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1578 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 426 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.44e+01 pdb=" N PRO B 427 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO B 427 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 427 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 178 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 457 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 458 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " -0.056 5.00e-02 4.00e+02 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1491 2.76 - 3.29: 10714 3.29 - 3.83: 18393 3.83 - 4.36: 21335 4.36 - 4.90: 35211 Nonbonded interactions: 87144 Sorted by model distance: nonbonded pdb=" O TYR A1038 " pdb=" OE1 GLN A1042 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 988 " pdb=" O LEU A1026 " model vdw 2.247 3.040 nonbonded pdb=" OG SER A 499 " pdb=" OE1 GLN A 582 " model vdw 2.253 3.040 nonbonded pdb=" O ASP A 895 " pdb=" OG1 THR A 898 " model vdw 2.257 3.040 nonbonded pdb=" OE2 GLU B 332 " pdb=" OH TYR B 431 " model vdw 2.268 3.040 ... (remaining 87139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.37 max=1.00 mean=0.99 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: 0.350 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 30.770 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 : 0.005 0.094 10859 Z= 0.327 Angle : 0.894 12.856 14651 Z= 0.455 Chirality : 0.051 0.219 1581 Planarity : 0.008 0.124 1883 Dihedral : 15.195 87.363 4196 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.59 % Allowed : 0.85 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.22), residues: 1281 helix: -0.71 (0.19), residues: 593 sheet: -1.80 (0.43), residues: 137 loop : -1.73 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 335 HIS 0.017 0.001 HIS A 940 PHE 0.035 0.003 PHE A 937 TYR 0.031 0.002 TYR A 165 ARG 0.016 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 526 ASN cc_start: 0.7934 (p0) cc_final: 0.7636 (p0) REVERT: A 988 TYR cc_start: 0.5782 (t80) cc_final: 0.5575 (t80) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 1.1333 time to fit residues: 375.2644 Evaluate side-chains 211 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.0030 chunk 64 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.5228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 HIS ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN A 160 HIS A 426 ASN A 661 GLN A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 785 ASN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10859 Z= 0.218 Angle : 0.753 12.050 14651 Z= 0.376 Chirality : 0.045 0.171 1581 Planarity : 0.006 0.087 1883 Dihedral : 6.206 70.255 1437 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.29 % Allowed : 17.44 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -1.31 (0.23), residues: 1281 helix: 0.10 (0.20), residues: 610 sheet: -1.75 (0.43), residues: 140 loop : -1.70 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 333 HIS 0.012 0.001 HIS A 940 PHE 0.040 0.002 PHE A 667 TYR 0.021 0.002 TYR A 432 ARG 0.010 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7509 (mpp) cc_final: 0.6432 (mpt) REVERT: A 330 ILE cc_start: 0.5860 (mt) cc_final: 0.5610 (mt) REVERT: A 391 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7252 (tp) REVERT: A 427 ILE cc_start: 0.8328 (mp) cc_final: 0.7946 (mt) REVERT: A 812 LEU cc_start: 0.7382 (tp) cc_final: 0.7081 (tp) REVERT: A 839 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6584 (tt) REVERT: A 1000 ASN cc_start: 0.6471 (t0) cc_final: 0.5987 (m-40) outliers start: 21 outliers final: 6 residues processed: 250 average time/residue: 0.9905 time to fit residues: 271.9251 Evaluate side-chains 226 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 218 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 840 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 GLN ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10859 Z= 0.263 Angle : 0.741 10.274 14651 Z= 0.371 Chirality : 0.046 0.288 1581 Planarity : 0.005 0.075 1883 Dihedral : 5.956 68.185 1437 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.39 % Allowed : 19.90 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -1.14 (0.23), residues: 1281 helix: 0.33 (0.21), residues: 612 sheet: -1.82 (0.43), residues: 142 loop : -1.70 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 333 HIS 0.009 0.001 HIS A 59 PHE 0.043 0.002 PHE A 667 TYR 0.022 0.002 TYR A 985 ARG 0.011 0.001 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 367 ASP cc_start: 0.6029 (m-30) cc_final: 0.5809 (m-30) REVERT: B 420 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5971 (mm) REVERT: B 479 MET cc_start: 0.6893 (pp-130) cc_final: 0.6591 (pp-130) REVERT: B 499 GLN cc_start: 0.7204 (tm130) cc_final: 0.6843 (tm130) REVERT: A 58 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6250 (mm) REVERT: A 123 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.4859 (pp-130) REVERT: A 330 ILE cc_start: 0.6131 (mt) cc_final: 0.5863 (mt) REVERT: A 391 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7353 (tp) REVERT: A 427 ILE cc_start: 0.8499 (mp) cc_final: 0.8087 (mt) REVERT: A 1000 ASN cc_start: 0.6639 (t0) cc_final: 0.5997 (m-40) outliers start: 34 outliers final: 12 residues processed: 254 average time/residue: 0.9878 time to fit residues: 275.9257 Evaluate side-chains 234 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 0.0970 chunk 33 optimal weight: 10.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10859 Z= 0.210 Angle : 0.714 10.868 14651 Z= 0.356 Chirality : 0.044 0.280 1581 Planarity : 0.005 0.069 1883 Dihedral : 5.807 65.049 1437 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.39 % Allowed : 21.76 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.97 (0.23), residues: 1281 helix: 0.48 (0.21), residues: 609 sheet: -1.75 (0.42), residues: 139 loop : -1.62 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 333 HIS 0.010 0.001 HIS A 59 PHE 0.043 0.002 PHE A 667 TYR 0.014 0.001 TYR A 432 ARG 0.012 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.5789 (OUTLIER) cc_final: 0.5471 (t) REVERT: B 479 MET cc_start: 0.6803 (pp-130) cc_final: 0.6558 (pp-130) REVERT: B 537 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: B 563 MET cc_start: 0.5967 (ppp) cc_final: 0.4411 (mtm) REVERT: A 58 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6249 (mm) REVERT: A 123 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5028 (pp-130) REVERT: A 164 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6651 (mpp) REVERT: A 258 ASP cc_start: 0.7912 (m-30) cc_final: 0.7705 (m-30) REVERT: A 330 ILE cc_start: 0.6128 (mt) cc_final: 0.5830 (mt) REVERT: A 391 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7321 (tp) REVERT: A 427 ILE cc_start: 0.8394 (mp) cc_final: 0.8019 (mt) REVERT: A 1000 ASN cc_start: 0.6528 (t0) cc_final: 0.6066 (m-40) outliers start: 34 outliers final: 15 residues processed: 249 average time/residue: 0.9360 time to fit residues: 257.5676 Evaluate side-chains 234 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN B 435 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10859 Z= 0.240 Angle : 0.728 11.353 14651 Z= 0.364 Chirality : 0.045 0.179 1581 Planarity : 0.005 0.066 1883 Dihedral : 5.687 60.739 1437 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.13 % Allowed : 23.54 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.96 (0.23), residues: 1281 helix: 0.48 (0.21), residues: 611 sheet: -1.93 (0.42), residues: 142 loop : -1.54 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 333 HIS 0.011 0.001 HIS A 59 PHE 0.042 0.002 PHE A 667 TYR 0.033 0.002 TYR A 985 ARG 0.009 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.5757 (OUTLIER) cc_final: 0.5430 (t) REVERT: B 479 MET cc_start: 0.6875 (pp-130) cc_final: 0.6634 (pp-130) REVERT: B 534 ARG cc_start: 0.7919 (tpt-90) cc_final: 0.7597 (tpt-90) REVERT: B 537 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: B 563 MET cc_start: 0.6161 (ppp) cc_final: 0.4534 (mtm) REVERT: A 58 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6375 (mm) REVERT: A 123 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5103 (pp-130) REVERT: A 427 ILE cc_start: 0.8587 (mp) cc_final: 0.8364 (mp) REVERT: A 641 TYR cc_start: 0.6492 (m-10) cc_final: 0.6180 (m-10) outliers start: 32 outliers final: 17 residues processed: 248 average time/residue: 1.0105 time to fit residues: 276.5536 Evaluate side-chains 238 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10859 Z= 0.261 Angle : 0.752 10.148 14651 Z= 0.375 Chirality : 0.046 0.295 1581 Planarity : 0.005 0.065 1883 Dihedral : 5.597 56.552 1437 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.81 % Allowed : 24.13 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.94 (0.23), residues: 1281 helix: 0.47 (0.21), residues: 612 sheet: -1.93 (0.42), residues: 137 loop : -1.49 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 333 HIS 0.011 0.001 HIS A 59 PHE 0.040 0.002 PHE A 667 TYR 0.023 0.002 TYR A 988 ARG 0.013 0.001 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.5857 (OUTLIER) cc_final: 0.5546 (t) REVERT: B 479 MET cc_start: 0.6906 (pp-130) cc_final: 0.6639 (pp-130) REVERT: B 534 ARG cc_start: 0.7939 (tpt-90) cc_final: 0.7731 (tpt-90) REVERT: B 537 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: B 563 MET cc_start: 0.6249 (ppp) cc_final: 0.4612 (mtm) REVERT: A 58 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6364 (mm) REVERT: A 123 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5114 (pp-130) REVERT: A 164 MET cc_start: 0.8044 (mpp) cc_final: 0.7820 (mpp) REVERT: A 296 GLN cc_start: 0.7565 (tp40) cc_final: 0.7310 (tp40) REVERT: A 391 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7386 (tp) REVERT: A 427 ILE cc_start: 0.8641 (mp) cc_final: 0.8356 (mp) REVERT: A 441 MET cc_start: 0.6874 (ppp) cc_final: 0.6606 (ppp) REVERT: A 875 HIS cc_start: 0.7322 (m-70) cc_final: 0.6583 (p-80) REVERT: A 909 PHE cc_start: 0.7699 (t80) cc_final: 0.7466 (t80) outliers start: 39 outliers final: 21 residues processed: 254 average time/residue: 0.8980 time to fit residues: 251.2258 Evaluate side-chains 250 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 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 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A1042 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10859 Z= 0.248 Angle : 0.775 10.911 14651 Z= 0.381 Chirality : 0.047 0.318 1581 Planarity : 0.005 0.064 1883 Dihedral : 5.495 51.601 1437 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.30 % Allowed : 25.06 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.96 (0.23), residues: 1281 helix: 0.50 (0.21), residues: 611 sheet: -2.13 (0.41), residues: 140 loop : -1.51 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 333 HIS 0.012 0.001 HIS A 59 PHE 0.041 0.002 PHE A 667 TYR 0.033 0.002 TYR A 985 ARG 0.009 0.001 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.5829 (OUTLIER) cc_final: 0.5534 (t) REVERT: B 479 MET cc_start: 0.6873 (pp-130) cc_final: 0.6535 (pp-130) REVERT: B 534 ARG cc_start: 0.7936 (tpt-90) cc_final: 0.7698 (tpt-90) REVERT: B 537 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: B 563 MET cc_start: 0.6231 (ppp) cc_final: 0.4617 (mtm) REVERT: A 58 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6361 (mm) REVERT: A 123 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5124 (pp-130) REVERT: A 391 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7293 (tp) REVERT: A 427 ILE cc_start: 0.8622 (mp) cc_final: 0.8185 (mt) REVERT: A 1042 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8087 (mp10) outliers start: 33 outliers final: 23 residues processed: 244 average time/residue: 0.9473 time to fit residues: 254.7517 Evaluate side-chains 249 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain A residue 1042 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 450 HIS ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 GLN ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10859 Z= 0.234 Angle : 0.777 9.840 14651 Z= 0.383 Chirality : 0.046 0.301 1581 Planarity : 0.005 0.063 1883 Dihedral : 5.383 47.088 1437 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.47 % Allowed : 25.74 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.89 (0.23), residues: 1281 helix: 0.57 (0.21), residues: 605 sheet: -2.12 (0.40), residues: 140 loop : -1.45 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 333 HIS 0.012 0.001 HIS A 59 PHE 0.042 0.002 PHE A 667 TYR 0.015 0.002 TYR A 904 ARG 0.008 0.001 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.5956 (OUTLIER) cc_final: 0.5634 (t) REVERT: B 479 MET cc_start: 0.6867 (pp-130) cc_final: 0.6539 (pp-130) REVERT: B 534 ARG cc_start: 0.7911 (tpt-90) cc_final: 0.7654 (tpt-90) REVERT: B 537 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: B 563 MET cc_start: 0.6238 (ppp) cc_final: 0.4621 (mtm) REVERT: A 58 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6350 (mm) REVERT: A 123 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5155 (pp-130) REVERT: A 391 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7162 (tp) REVERT: A 427 ILE cc_start: 0.8601 (mp) cc_final: 0.8171 (mt) outliers start: 35 outliers final: 23 residues processed: 244 average time/residue: 0.9824 time to fit residues: 263.4515 Evaluate side-chains 251 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1001 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 68 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.253 10859 Z= 0.426 Angle : 1.180 59.188 14651 Z= 0.621 Chirality : 0.050 0.464 1581 Planarity : 0.006 0.138 1883 Dihedral : 5.393 47.037 1437 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 3.13 % Allowed : 26.25 % Favored : 70.62 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.92 % 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: -0.92 (0.23), residues: 1281 helix: 0.52 (0.21), residues: 605 sheet: -2.12 (0.40), residues: 140 loop : -1.45 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 333 HIS 0.009 0.001 HIS A 59 PHE 0.040 0.002 PHE A 667 TYR 0.020 0.002 TYR A 432 ARG 0.006 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.5951 (OUTLIER) cc_final: 0.5636 (t) REVERT: B 479 MET cc_start: 0.6866 (pp-130) cc_final: 0.6534 (pp-130) REVERT: B 534 ARG cc_start: 0.7909 (tpt-90) cc_final: 0.7650 (tpt-90) REVERT: B 537 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: B 563 MET cc_start: 0.6234 (ppp) cc_final: 0.4619 (mtm) REVERT: A 58 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6350 (mm) REVERT: A 123 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.5136 (pp-130) REVERT: A 296 GLN cc_start: 0.7309 (tp40) cc_final: 0.6125 (mt0) REVERT: A 391 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7173 (tp) REVERT: A 427 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 441 MET cc_start: 0.6983 (ppp) cc_final: 0.6453 (ppp) outliers start: 31 outliers final: 23 residues processed: 238 average time/residue: 0.9821 time to fit residues: 257.8210 Evaluate side-chains 248 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain A residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.253 10859 Z= 0.426 Angle : 1.180 59.187 14651 Z= 0.621 Chirality : 0.050 0.464 1581 Planarity : 0.006 0.138 1883 Dihedral : 5.393 47.037 1437 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 2.96 % Allowed : 26.84 % Favored : 70.19 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.92 % 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: -0.92 (0.23), residues: 1281 helix: 0.52 (0.21), residues: 605 sheet: -2.12 (0.40), residues: 140 loop : -1.45 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 333 HIS 0.009 0.001 HIS A 59 PHE 0.040 0.002 PHE A 667 TYR 0.020 0.002 TYR A 432 ARG 0.006 0.000 ARG B 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 422 VAL cc_start: 0.5954 (OUTLIER) cc_final: 0.5637 (t) REVERT: B 479 MET cc_start: 0.6866 (pp-130) cc_final: 0.6534 (pp-130) REVERT: B 534 ARG cc_start: 0.7913 (tpt-90) cc_final: 0.7650 (tpt-90) REVERT: B 537 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: B 563 MET cc_start: 0.6234 (ppp) cc_final: 0.4619 (mtm) REVERT: A 58 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6350 (mm) REVERT: A 123 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5136 (pp-130) REVERT: A 296 GLN cc_start: 0.7306 (tp40) cc_final: 0.6125 (mt0) REVERT: A 391 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7173 (tp) REVERT: A 427 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 441 MET cc_start: 0.6982 (ppp) cc_final: 0.6453 (ppp) outliers start: 29 outliers final: 23 residues processed: 234 average time/residue: 0.9600 time to fit residues: 247.7551 Evaluate side-chains 246 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain A residue 1001 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.0050 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.215790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.177634 restraints weight = 36568.719| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 4.80 r_work: 0.4191 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4135 r_free = 0.4135 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.253 10859 Z= 0.426 Angle : 1.180 59.187 14651 Z= 0.621 Chirality : 0.050 0.464 1581 Planarity : 0.006 0.138 1883 Dihedral : 5.393 47.037 1437 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 2.96 % Allowed : 26.93 % Favored : 70.11 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.92 % 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: -0.92 (0.23), residues: 1281 helix: 0.52 (0.21), residues: 605 sheet: -2.12 (0.40), residues: 140 loop : -1.45 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 333 HIS 0.009 0.001 HIS A 59 PHE 0.040 0.002 PHE A 667 TYR 0.020 0.002 TYR A 432 ARG 0.006 0.000 ARG B 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4450.85 seconds wall clock time: 80 minutes 55.79 seconds (4855.79 seconds total)