Starting phenix.real_space_refine on Fri Sep 27 12:15:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/09_2024/6xmx_22265_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/09_2024/6xmx_22265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/09_2024/6xmx_22265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/09_2024/6xmx_22265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/09_2024/6xmx_22265_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xmx_22265/09_2024/6xmx_22265_trim.cif" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 88 5.16 5 Cl 8 4.86 5 C 5136 2.51 5 N 1408 2.21 5 O 1432 1.98 5 H 7942 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16014 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "B" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "C" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "G" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "H" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.04, per 1000 atoms: 0.50 Number of scatterers: 16014 At special positions: 0 Unit cell: (137.775, 77.55, 113.025, 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) Cl 8 17.00 S 88 16.00 O 1432 8.00 N 1408 7.00 C 5136 6.00 H 7942 1.00 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: 4.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 68.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.670A pdb=" N ASP B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'C' and resid 13 through 28 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.670A pdb=" N ASP C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'D' and resid 13 through 28 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'E' and resid 13 through 28 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN E 68 " --> pdb=" O GLN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'F' and resid 13 through 28 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 54 through 63 removed outlier: 3.670A pdb=" N ASP F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN F 68 " --> pdb=" O GLN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 114 through 128 Processing helix chain 'G' and resid 13 through 28 Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 removed outlier: 4.785A pdb=" N ASN G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 114 through 128 Processing helix chain 'H' and resid 13 through 28 Processing helix chain 'H' and resid 46 through 54 Processing helix chain 'H' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN H 68 " --> pdb=" O GLN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 114 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.675A pdb=" N ILE A 9 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 95 " --> pdb=" O ILE A 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 45 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 4.289A pdb=" N LEU A 95 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 9 " --> pdb=" O LEU A 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 45 Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 removed outlier: 4.280A pdb=" N ILE C 9 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 95 " --> pdb=" O ILE C 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 45 Processing sheet with id=AA7, first strand: chain 'D' and resid 41 through 45 Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.430A pdb=" N ILE E 9 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU F 95 " --> pdb=" O ILE E 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 41 through 45 Processing sheet with id=AB1, first strand: chain 'E' and resid 94 through 95 removed outlier: 3.505A pdb=" N ILE F 9 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 41 through 45 Processing sheet with id=AB3, first strand: chain 'G' and resid 9 through 10 removed outlier: 4.572A pdb=" N ILE G 9 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU H 95 " --> pdb=" O ILE G 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=AB5, first strand: chain 'G' and resid 94 through 95 removed outlier: 4.179A pdb=" N LEU G 95 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE H 9 " --> pdb=" O LEU G 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 41 through 45 497 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7903 1.02 - 1.21: 39 1.21 - 1.41: 3312 1.41 - 1.61: 4752 1.61 - 1.80: 144 Bond restraints: 16150 Sorted by residual: bond pdb=" C24 U52 A 401 " pdb=" N20 U52 A 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 D 401 " pdb=" N20 U52 D 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 G 401 " pdb=" N20 U52 G 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 C 401 " pdb=" N20 U52 C 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C24 U52 B 401 " pdb=" N20 U52 B 401 " ideal model delta sigma weight residual 1.352 1.424 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 16145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.56: 28983 6.56 - 13.13: 21 13.13 - 19.69: 5 19.69 - 26.26: 1 26.26 - 32.82: 4 Bond angle restraints: 29014 Sorted by residual: angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB2 GLU A 81 " ideal model delta sigma weight residual 109.00 76.18 32.82 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 109.00 77.25 31.75 3.00e+00 1.11e-01 1.12e+02 angle pdb=" HB2 GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 110.00 138.13 -28.13 3.00e+00 1.11e-01 8.79e+01 angle pdb=" CG GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB2 GLU A 81 " ideal model delta sigma weight residual 108.00 81.68 26.32 3.00e+00 1.11e-01 7.70e+01 angle pdb=" CG GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 108.00 83.18 24.82 3.00e+00 1.11e-01 6.85e+01 ... (remaining 29009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6763 16.69 - 33.38: 562 33.38 - 50.07: 185 50.07 - 66.76: 78 66.76 - 83.45: 18 Dihedral angle restraints: 7606 sinusoidal: 4286 harmonic: 3320 Sorted by residual: dihedral pdb=" N GLU H 81 " pdb=" CA GLU H 81 " pdb=" CB GLU H 81 " pdb=" CG GLU H 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.59 50.41 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" N GLU D 81 " pdb=" CA GLU D 81 " pdb=" CB GLU D 81 " pdb=" CG GLU D 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.61 50.39 3 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" N GLU B 81 " pdb=" CA GLU B 81 " pdb=" CB GLU B 81 " pdb=" CG GLU B 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.61 50.39 3 1.50e+01 4.44e-03 8.89e+00 ... (remaining 7603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 683 0.034 - 0.067: 325 0.067 - 0.100: 172 0.100 - 0.134: 84 0.134 - 0.167: 32 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CB VAL C 117 " pdb=" CA VAL C 117 " pdb=" CG1 VAL C 117 " pdb=" CG2 VAL C 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CB VAL E 117 " pdb=" CA VAL E 117 " pdb=" CG1 VAL E 117 " pdb=" CG2 VAL E 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PRO E 80 " pdb=" N PRO E 80 " pdb=" C PRO E 80 " pdb=" CB PRO E 80 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1293 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 43 " 0.015 2.00e-02 2.50e+03 1.41e-02 6.00e+00 pdb=" CG PHE B 43 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 43 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 43 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE B 43 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE B 43 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 43 " -0.014 2.00e-02 2.50e+03 1.39e-02 5.81e+00 pdb=" CG PHE E 43 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 43 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE E 43 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 43 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 43 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 43 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE E 43 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE E 43 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE E 43 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE E 43 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE E 43 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 43 " 0.016 2.00e-02 2.50e+03 1.37e-02 5.60e+00 pdb=" CG PHE D 43 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE D 43 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE D 43 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 43 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 43 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE D 43 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE D 43 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE D 43 " -0.002 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 188 2.04 - 2.68: 25536 2.68 - 3.32: 46659 3.32 - 3.96: 59609 3.96 - 4.60: 94945 Nonbonded interactions: 226937 Sorted by model distance: nonbonded pdb=" O TYR A 58 " pdb=" HG1 THR A 62 " model vdw 1.397 2.450 nonbonded pdb=" O TYR B 58 " pdb=" HG1 THR B 62 " model vdw 1.483 2.450 nonbonded pdb=" O TYR C 58 " pdb=" HG1 THR C 62 " model vdw 1.504 2.450 nonbonded pdb=" O TYR G 58 " pdb=" HG1 THR G 62 " model vdw 1.534 2.450 nonbonded pdb=" O THR G 92 " pdb=" HG SER G 93 " model vdw 1.539 2.450 ... (remaining 226932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 128 or resid 401)) selection = (chain 'B' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'C' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'D' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'E' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'F' and (resid 7 through 107 or (resid 108 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) \ selection = (chain 'G' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) selection = (chain 'H' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 128 or resid 401)) } 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: 1.280 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: 0.260 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.880 Find NCS groups from input model: 0.690 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5250 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 0.083 8208 Z= 0.754 Angle : 1.120 9.615 11096 Z= 0.621 Chirality : 0.057 0.167 1296 Planarity : 0.006 0.023 1368 Dihedral : 15.974 83.454 3168 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.89 % Allowed : 5.36 % Favored : 93.75 % 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: -1.34 (0.23), residues: 960 helix: -1.09 (0.16), residues: 584 sheet: None (None), residues: 0 loop : -0.24 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.005 HIS G 46 PHE 0.040 0.005 PHE B 43 TYR 0.016 0.004 TYR E 111 ARG 0.025 0.003 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 299 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ILE cc_start: 0.6262 (mt) cc_final: 0.5823 (mt) REVERT: D 105 VAL cc_start: 0.6412 (t) cc_final: 0.6160 (t) REVERT: F 30 ILE cc_start: 0.5867 (mt) cc_final: 0.5556 (mt) outliers start: 8 outliers final: 2 residues processed: 304 average time/residue: 0.4385 time to fit residues: 179.0498 Evaluate side-chains 166 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8208 Z= 0.174 Angle : 0.551 9.049 11096 Z= 0.305 Chirality : 0.042 0.154 1296 Planarity : 0.003 0.027 1368 Dihedral : 6.193 54.481 1286 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.79 % Allowed : 15.29 % Favored : 82.92 % 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: 1.25 (0.27), residues: 960 helix: 1.30 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.17 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 46 PHE 0.020 0.001 PHE H 124 TYR 0.016 0.002 TYR B 58 ARG 0.006 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 SER cc_start: 0.7294 (t) cc_final: 0.6981 (m) REVERT: C 86 LEU cc_start: 0.7061 (mt) cc_final: 0.6818 (mt) REVERT: D 30 ILE cc_start: 0.6150 (mt) cc_final: 0.5899 (mt) outliers start: 16 outliers final: 9 residues processed: 198 average time/residue: 0.3736 time to fit residues: 103.9904 Evaluate side-chains 169 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 21 ASN D 23 ASN D 42 GLN F 96 ASN G 113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8208 Z= 0.299 Angle : 0.666 8.472 11096 Z= 0.366 Chirality : 0.045 0.181 1296 Planarity : 0.005 0.058 1368 Dihedral : 8.151 61.102 1283 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.68 % Allowed : 15.74 % Favored : 81.58 % 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: 0.88 (0.27), residues: 960 helix: 1.08 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.13 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 14 PHE 0.016 0.002 PHE D 89 TYR 0.021 0.003 TYR E 58 ARG 0.006 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: D 30 ILE cc_start: 0.6253 (mt) cc_final: 0.6034 (mt) REVERT: H 22 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.4963 (tt) REVERT: H 26 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5950 (ttt90) outliers start: 24 outliers final: 13 residues processed: 193 average time/residue: 0.3921 time to fit residues: 105.3435 Evaluate side-chains 178 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 26 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8208 Z= 0.224 Angle : 0.574 8.187 11096 Z= 0.316 Chirality : 0.042 0.161 1296 Planarity : 0.003 0.037 1368 Dihedral : 7.299 57.971 1280 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.23 % Allowed : 16.41 % Favored : 81.36 % 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: 1.05 (0.27), residues: 960 helix: 1.25 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.13 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 46 PHE 0.013 0.001 PHE F 124 TYR 0.017 0.002 TYR A 58 ARG 0.003 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 MET cc_start: 0.6949 (mmt) cc_final: 0.6329 (mpp) REVERT: G 106 MET cc_start: 0.7097 (tpt) cc_final: 0.6648 (tpt) REVERT: H 22 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.4956 (tt) REVERT: H 26 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6056 (ttt90) REVERT: H 110 MET cc_start: 0.6192 (mtm) cc_final: 0.5949 (mtt) outliers start: 20 outliers final: 13 residues processed: 187 average time/residue: 0.4063 time to fit residues: 104.8112 Evaluate side-chains 176 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 26 ARG Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 102 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.7340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8208 Z= 0.291 Angle : 0.646 8.353 11096 Z= 0.356 Chirality : 0.044 0.175 1296 Planarity : 0.004 0.046 1368 Dihedral : 7.864 59.270 1280 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.35 % Allowed : 15.74 % Favored : 80.92 % 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: 0.69 (0.26), residues: 960 helix: 0.95 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.24 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 14 PHE 0.013 0.002 PHE D 89 TYR 0.024 0.003 TYR A 58 ARG 0.003 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.4870 (mp0) REVERT: D 103 MET cc_start: 0.7016 (mmt) cc_final: 0.6532 (mpp) REVERT: F 106 MET cc_start: 0.5500 (ttt) cc_final: 0.5120 (mtt) REVERT: G 106 MET cc_start: 0.7234 (tpt) cc_final: 0.7006 (tpt) REVERT: H 22 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5119 (tt) REVERT: H 26 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6018 (ttt90) outliers start: 30 outliers final: 24 residues processed: 185 average time/residue: 0.4185 time to fit residues: 105.7171 Evaluate side-chains 190 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain G residue 124 PHE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 26 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.7534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8208 Z= 0.161 Angle : 0.532 9.091 11096 Z= 0.286 Chirality : 0.041 0.144 1296 Planarity : 0.003 0.040 1368 Dihedral : 6.964 61.098 1280 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.67 % Allowed : 17.97 % Favored : 80.36 % 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: 1.37 (0.27), residues: 960 helix: 1.52 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.02 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 46 PHE 0.012 0.001 PHE C 83 TYR 0.034 0.002 TYR A 58 ARG 0.006 0.000 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.5910 (mt) cc_final: 0.5388 (mt) REVERT: D 103 MET cc_start: 0.6933 (mmt) cc_final: 0.6407 (mpp) REVERT: F 106 MET cc_start: 0.5420 (ttt) cc_final: 0.4980 (mtt) REVERT: H 22 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.4958 (tt) REVERT: H 26 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5913 (ttt90) REVERT: H 110 MET cc_start: 0.6106 (mtm) cc_final: 0.5776 (mtt) outliers start: 15 outliers final: 11 residues processed: 180 average time/residue: 0.4268 time to fit residues: 105.3556 Evaluate side-chains 175 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 26 ARG Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 0.0980 chunk 55 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.7736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8208 Z= 0.153 Angle : 0.518 8.716 11096 Z= 0.276 Chirality : 0.041 0.141 1296 Planarity : 0.003 0.040 1368 Dihedral : 6.985 70.892 1280 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.45 % Allowed : 18.30 % Favored : 80.25 % 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: 1.76 (0.27), residues: 960 helix: 1.84 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.12 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 46 PHE 0.008 0.001 PHE G 83 TYR 0.030 0.002 TYR A 58 ARG 0.004 0.000 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.5889 (mt) cc_final: 0.5405 (mt) REVERT: D 103 MET cc_start: 0.6910 (mmt) cc_final: 0.6354 (mpp) REVERT: F 106 MET cc_start: 0.5390 (ttt) cc_final: 0.4932 (mtt) REVERT: G 106 MET cc_start: 0.7027 (tpt) cc_final: 0.6636 (tpt) REVERT: H 22 LEU cc_start: 0.5361 (OUTLIER) cc_final: 0.4951 (tt) outliers start: 13 outliers final: 8 residues processed: 179 average time/residue: 0.4153 time to fit residues: 101.8351 Evaluate side-chains 173 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 22 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8208 Z= 0.215 Angle : 0.567 8.186 11096 Z= 0.305 Chirality : 0.042 0.157 1296 Planarity : 0.004 0.043 1368 Dihedral : 7.429 75.183 1280 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.23 % Allowed : 17.86 % Favored : 79.91 % 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: 1.54 (0.27), residues: 960 helix: 1.67 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.01 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 14 PHE 0.015 0.001 PHE B 124 TYR 0.027 0.002 TYR A 58 ARG 0.006 0.000 ARG H 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 MET cc_start: 0.6951 (mmt) cc_final: 0.6462 (mpp) REVERT: F 106 MET cc_start: 0.5537 (ttt) cc_final: 0.5037 (mtt) REVERT: G 106 MET cc_start: 0.7126 (tpt) cc_final: 0.6720 (tpt) REVERT: H 22 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5088 (tt) outliers start: 20 outliers final: 17 residues processed: 171 average time/residue: 0.4567 time to fit residues: 109.1778 Evaluate side-chains 178 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain G residue 124 PHE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.8134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8208 Z= 0.153 Angle : 0.519 9.158 11096 Z= 0.276 Chirality : 0.041 0.138 1296 Planarity : 0.003 0.044 1368 Dihedral : 7.149 76.007 1280 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 19.20 % Favored : 79.35 % 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: 1.86 (0.27), residues: 960 helix: 1.91 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.15 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 46 PHE 0.008 0.001 PHE G 83 TYR 0.028 0.002 TYR A 58 ARG 0.008 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.5629 (mt) cc_final: 0.5059 (mt) REVERT: D 103 MET cc_start: 0.6936 (mmt) cc_final: 0.6483 (mpp) REVERT: F 106 MET cc_start: 0.5533 (ttt) cc_final: 0.5043 (mtt) REVERT: G 106 MET cc_start: 0.7097 (tpt) cc_final: 0.6639 (tpt) REVERT: H 22 LEU cc_start: 0.5475 (OUTLIER) cc_final: 0.5071 (tt) outliers start: 13 outliers final: 12 residues processed: 173 average time/residue: 0.4142 time to fit residues: 98.0302 Evaluate side-chains 174 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.8265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8208 Z= 0.154 Angle : 0.531 8.831 11096 Z= 0.279 Chirality : 0.041 0.139 1296 Planarity : 0.003 0.051 1368 Dihedral : 7.165 75.793 1280 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 19.08 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.27), residues: 960 helix: 2.03 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.19 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 14 PHE 0.013 0.001 PHE C 83 TYR 0.025 0.002 TYR A 58 ARG 0.006 0.000 ARG H 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.5598 (mt) cc_final: 0.5055 (mt) REVERT: D 103 MET cc_start: 0.6945 (mmt) cc_final: 0.6437 (mpp) REVERT: F 106 MET cc_start: 0.5489 (ttt) cc_final: 0.5010 (mtt) REVERT: G 106 MET cc_start: 0.7088 (tpt) cc_final: 0.6620 (tpt) REVERT: H 22 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5042 (tt) outliers start: 13 outliers final: 12 residues processed: 178 average time/residue: 0.4162 time to fit residues: 102.2979 Evaluate side-chains 176 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.0970 chunk 9 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.202627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.180522 restraints weight = 27261.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.186467 restraints weight = 12303.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.189917 restraints weight = 6767.203| |-----------------------------------------------------------------------------| r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.8306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8208 Z= 0.139 Angle : 0.517 9.169 11096 Z= 0.271 Chirality : 0.041 0.135 1296 Planarity : 0.003 0.051 1368 Dihedral : 7.006 75.532 1280 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.00 % Allowed : 19.75 % Favored : 79.24 % 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 (0.27), residues: 960 helix: 2.19 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.29 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 46 PHE 0.007 0.001 PHE G 83 TYR 0.025 0.001 TYR A 58 ARG 0.006 0.000 ARG H 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3999.58 seconds wall clock time: 70 minutes 12.07 seconds (4212.07 seconds total)