Starting phenix.real_space_refine on Fri Oct 23 08:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sec_54806/10_2026/9sec_54806.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sec_54806/10_2026/9sec_54806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sec_54806/10_2026/9sec_54806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sec_54806/10_2026/9sec_54806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sec_54806/10_2026/9sec_54806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sec_54806/10_2026/9sec_54806.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 P 7 5.49 5 S 21 5.16 5 C 6426 2.51 5 N 1274 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9289 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1188 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "B" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1188 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1188 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "D" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1188 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "E" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1188 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "F" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1188 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1188 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 139 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 2, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 139 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 2, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 149 Unusual residues: {'C14': 3, 'D10': 3, 'D12': 2, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 129 Unusual residues: {'C14': 3, 'D10': 1, 'D12': 2, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 125 Unusual residues: {'C14': 2, 'D10': 2, 'D12': 2, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "F" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 153 Unusual residues: {'C14': 4, 'D10': 2, 'D12': 2, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "G" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 139 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 2, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Time building chain proxies: 2.08, per 1000 atoms: 0.22 Number of scatterers: 9289 At special positions: 0 Unit cell: (85.14, 87.032, 96.492, 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 21 16.00 P 7 15.00 O 1561 8.00 N 1274 7.00 C 6426 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: 0.84 Conformation dependent library (CDL) restraints added in 322.4 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 65.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 7 through 41 removed outlier: 4.424A pdb=" N PHE A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 72 Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 93 through 109 removed outlier: 4.053A pdb=" N TYR A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'B' and resid 7 through 41 removed outlier: 4.424A pdb=" N PHE B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 72 Processing helix chain 'B' and resid 75 through 92 Processing helix chain 'B' and resid 93 through 109 removed outlier: 4.053A pdb=" N TYR B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'C' and resid 7 through 41 removed outlier: 4.425A pdb=" N PHE C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 Processing helix chain 'C' and resid 75 through 92 Processing helix chain 'C' and resid 93 through 109 removed outlier: 4.053A pdb=" N TYR C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'D' and resid 7 through 41 removed outlier: 4.425A pdb=" N PHE D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 72 Processing helix chain 'D' and resid 75 through 92 Processing helix chain 'D' and resid 93 through 109 removed outlier: 4.053A pdb=" N TYR D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'E' and resid 7 through 41 removed outlier: 4.424A pdb=" N PHE E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 72 Processing helix chain 'E' and resid 75 through 92 Processing helix chain 'E' and resid 93 through 109 removed outlier: 4.053A pdb=" N TYR E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'F' and resid 7 through 41 removed outlier: 4.425A pdb=" N PHE F 11 " --> pdb=" O ASN F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 72 Processing helix chain 'F' and resid 75 through 92 Processing helix chain 'F' and resid 93 through 109 removed outlier: 4.053A pdb=" N TYR F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'G' and resid 7 through 41 removed outlier: 4.424A pdb=" N PHE G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 Processing helix chain 'G' and resid 75 through 92 Processing helix chain 'G' and resid 93 through 109 removed outlier: 4.054A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 6.811A pdb=" N TYR B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE B 130 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS B 136 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 130 removed outlier: 6.795A pdb=" N LYS A 136 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE A 130 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.811A pdb=" N TYR C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE C 130 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS C 136 " --> pdb=" O LYS C 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 120 removed outlier: 6.811A pdb=" N TYR D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE D 130 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS D 136 " --> pdb=" O LYS D 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 118 through 120 removed outlier: 6.811A pdb=" N TYR E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE E 130 " --> pdb=" O TYR E 134 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS E 136 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 120 removed outlier: 6.812A pdb=" N TYR F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE F 130 " --> pdb=" O TYR F 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS F 136 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 118 through 120 removed outlier: 6.811A pdb=" N TYR G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE G 130 " --> pdb=" O TYR G 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS G 136 " --> pdb=" O LYS G 128 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1926 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: 1.12 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1317 1.32 - 1.44: 2135 1.44 - 1.56: 5858 1.56 - 1.68: 14 1.68 - 1.81: 35 Bond restraints: 9359 Sorted by residual: bond pdb=" C38 PEE A 201 " pdb=" C39 PEE A 201 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C38 PEE F 202 " pdb=" C39 PEE F 202 " ideal model delta sigma weight residual 1.523 1.315 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C38 PEE E 201 " pdb=" C39 PEE E 201 " ideal model delta sigma weight residual 1.523 1.315 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C38 PEE G 206 " pdb=" C39 PEE G 206 " ideal model delta sigma weight residual 1.523 1.315 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C38 PEE B 201 " pdb=" C39 PEE B 201 " ideal model delta sigma weight residual 1.523 1.315 0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 9354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 12254 2.97 - 5.94: 73 5.94 - 8.91: 7 8.91 - 11.89: 7 11.89 - 14.86: 14 Bond angle restraints: 12355 Sorted by residual: angle pdb=" C38 PEE A 201 " pdb=" C39 PEE A 201 " pdb=" C40 PEE A 201 " ideal model delta sigma weight residual 112.47 127.33 -14.86 3.00e+00 1.11e-01 2.45e+01 angle pdb=" C38 PEE F 202 " pdb=" C39 PEE F 202 " pdb=" C40 PEE F 202 " ideal model delta sigma weight residual 112.47 127.28 -14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C38 PEE E 201 " pdb=" C39 PEE E 201 " pdb=" C40 PEE E 201 " ideal model delta sigma weight residual 112.47 127.27 -14.80 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C38 PEE C 201 " pdb=" C39 PEE C 201 " pdb=" C40 PEE C 201 " ideal model delta sigma weight residual 112.47 127.26 -14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C38 PEE G 206 " pdb=" C39 PEE G 206 " pdb=" C40 PEE G 206 " ideal model delta sigma weight residual 112.47 127.25 -14.78 3.00e+00 1.11e-01 2.43e+01 ... (remaining 12350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.37: 5547 29.37 - 58.74: 102 58.74 - 88.11: 28 88.11 - 117.48: 0 117.48 - 146.85: 14 Dihedral angle restraints: 5691 sinusoidal: 2555 harmonic: 3136 Sorted by residual: dihedral pdb=" C4 PEE E 201 " pdb=" O4P PEE E 201 " pdb=" P PEE E 201 " pdb=" O3P PEE E 201 " ideal model delta sinusoidal sigma weight residual 171.78 -41.37 -146.85 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C4 PEE G 206 " pdb=" O4P PEE G 206 " pdb=" P PEE G 206 " pdb=" O3P PEE G 206 " ideal model delta sinusoidal sigma weight residual 171.78 -41.38 -146.84 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C4 PEE A 201 " pdb=" O4P PEE A 201 " pdb=" P PEE A 201 " pdb=" O3P PEE A 201 " ideal model delta sinusoidal sigma weight residual 171.78 -41.39 -146.83 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 5688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1154 0.047 - 0.093: 226 0.093 - 0.139: 83 0.139 - 0.186: 0 0.186 - 0.232: 7 Chirality restraints: 1470 Sorted by residual: chirality pdb=" C2 PEE F 202 " pdb=" C1 PEE F 202 " pdb=" C3 PEE F 202 " pdb=" O2 PEE F 202 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C2 PEE B 201 " pdb=" C1 PEE B 201 " pdb=" C3 PEE B 201 " pdb=" O2 PEE B 201 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C2 PEE E 201 " pdb=" C1 PEE E 201 " pdb=" C3 PEE E 201 " pdb=" O2 PEE E 201 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1467 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 87 " 0.020 2.00e-02 2.50e+03 2.75e-02 1.33e+01 pdb=" CG PHE B 87 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 87 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE B 87 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 87 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE B 87 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 87 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 87 " 0.020 2.00e-02 2.50e+03 2.75e-02 1.33e+01 pdb=" CG PHE A 87 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 87 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE A 87 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 87 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 87 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 87 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 87 " -0.020 2.00e-02 2.50e+03 2.75e-02 1.32e+01 pdb=" CG PHE E 87 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE E 87 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE E 87 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 87 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE E 87 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE E 87 " -0.004 2.00e-02 2.50e+03 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1582 2.77 - 3.30: 8673 3.30 - 3.84: 14601 3.84 - 4.37: 17909 4.37 - 4.90: 31644 Nonbonded interactions: 74409 Sorted by model distance: nonbonded pdb=" NH1 ARG A 159 " pdb=" OE1 GLU B 144 " model vdw 2.239 3.120 nonbonded pdb=" NH1 ARG F 159 " pdb=" OE1 GLU G 144 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG C 159 " pdb=" OE1 GLU D 144 " model vdw 2.287 3.120 nonbonded pdb=" O ALA B 107 " pdb=" NZ LYS B 110 " model vdw 2.339 3.120 nonbonded pdb=" O ALA F 107 " pdb=" NZ LYS F 110 " model vdw 2.339 3.120 ... (remaining 74404 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 6 through 162) selection = (chain 'B' and resid 6 through 162) selection = (chain 'C' and resid 6 through 162) selection = (chain 'D' and resid 6 through 162) selection = (chain 'E' and resid 6 through 162) selection = (chain 'F' and resid 6 through 162) selection = (chain 'G' and resid 6 through 162) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 8.710 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.209 9359 Z= 0.383 Angle : 0.747 14.858 12355 Z= 0.313 Chirality : 0.044 0.232 1470 Planarity : 0.003 0.028 1379 Dihedral : 14.747 146.853 3689 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.26), residues: 1085 helix: 2.89 (0.19), residues: 721 sheet: 1.25 (0.64), residues: 70 loop : -0.79 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 159 TYR 0.010 0.001 TYR G 43 PHE 0.060 0.003 PHE B 87 TRP 0.001 0.000 TRP E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.38 ( 9359) covalent geometry : angle 0.74669 / 0.31 (12355) hydrogen bonds : bond 0.10276 / 6.86 ( 658) hydrogen bonds : angle 5.07598 / 3.77 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.293 Fit side-chains REVERT: A 124 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8108 (mtpt) REVERT: A 132 PHE cc_start: 0.8378 (t80) cc_final: 0.8167 (t80) REVERT: B 124 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8060 (mtpt) REVERT: C 45 LYS cc_start: 0.7479 (mmtt) cc_final: 0.7059 (mtpt) REVERT: C 124 LYS cc_start: 0.8467 (mmtp) cc_final: 0.8002 (mtpt) REVERT: E 116 GLU cc_start: 0.8474 (pt0) cc_final: 0.8246 (pt0) REVERT: G 45 LYS cc_start: 0.7307 (mmtt) cc_final: 0.7021 (mptt) REVERT: G 55 VAL cc_start: 0.8393 (t) cc_final: 0.8168 (m) REVERT: G 116 GLU cc_start: 0.8465 (pt0) cc_final: 0.8134 (pt0) REVERT: G 132 PHE cc_start: 0.8229 (t80) cc_final: 0.7847 (t80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.6052 time to fit residues: 90.7999 Evaluate side-chains 98 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.161718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.127550 restraints weight = 10924.153| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.17 r_work: 0.3678 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9359 Z= 0.145 Angle : 0.561 8.526 12355 Z= 0.275 Chirality : 0.043 0.126 1470 Planarity : 0.003 0.025 1379 Dihedral : 15.617 147.753 1890 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.07 % Allowed : 6.29 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.26), residues: 1085 helix: 2.73 (0.19), residues: 721 sheet: -0.70 (0.52), residues: 105 loop : -1.09 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 159 TYR 0.019 0.002 TYR C 56 PHE 0.026 0.002 PHE C 87 TRP 0.001 0.000 TRP C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 9359) covalent geometry : angle 0.56065 / 0.28 (12355) hydrogen bonds : bond 0.04401 / 2.96 ( 658) hydrogen bonds : angle 3.97646 / 2.87 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.238 Fit side-chains REVERT: A 116 GLU cc_start: 0.8490 (pt0) cc_final: 0.8273 (pt0) REVERT: B 132 PHE cc_start: 0.8565 (t80) cc_final: 0.8257 (t80) REVERT: C 82 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8249 (mp) REVERT: C 159 ARG cc_start: 0.8097 (mtp-110) cc_final: 0.7828 (mtp85) REVERT: D 119 ASP cc_start: 0.7981 (t70) cc_final: 0.7740 (t0) REVERT: D 144 GLU cc_start: 0.8167 (tt0) cc_final: 0.7908 (tm-30) REVERT: E 116 GLU cc_start: 0.8458 (pt0) cc_final: 0.8166 (pt0) REVERT: E 159 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7746 (mtm110) REVERT: F 144 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: G 116 GLU cc_start: 0.8448 (pt0) cc_final: 0.8218 (pt0) REVERT: G 132 PHE cc_start: 0.8466 (t80) cc_final: 0.7780 (t80) outliers start: 10 outliers final: 3 residues processed: 123 average time/residue: 0.5053 time to fit residues: 66.9046 Evaluate side-chains 96 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 150 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [99, 72, 11, 103, 66, 28, 65, 59, 20, 58, 77] chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.161080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125740 restraints weight = 10909.581| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.24 r_work: 0.3675 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9359 Z= 0.134 Angle : 0.536 11.850 12355 Z= 0.257 Chirality : 0.042 0.122 1470 Planarity : 0.003 0.025 1379 Dihedral : 15.243 156.585 1890 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.49 % Allowed : 9.28 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.25), residues: 1085 helix: 2.68 (0.18), residues: 721 sheet: -0.37 (0.49), residues: 105 loop : -1.25 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.018 0.001 TYR E 56 PHE 0.012 0.001 PHE C 87 TRP 0.002 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9359) covalent geometry : angle 0.53576 / 0.26 (12355) hydrogen bonds : bond 0.04174 / 2.81 ( 658) hydrogen bonds : angle 3.67808 / 2.67 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.354 Fit side-chains REVERT: A 116 GLU cc_start: 0.8530 (pt0) cc_final: 0.8296 (pt0) REVERT: B 132 PHE cc_start: 0.8570 (t80) cc_final: 0.8176 (t80) REVERT: B 144 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: C 124 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8061 (mtpt) REVERT: C 159 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7796 (mtp85) REVERT: D 144 GLU cc_start: 0.8190 (tt0) cc_final: 0.7909 (tm-30) REVERT: E 116 GLU cc_start: 0.8557 (pt0) cc_final: 0.8282 (pt0) REVERT: G 30 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7293 (mtmm) REVERT: G 116 GLU cc_start: 0.8479 (pt0) cc_final: 0.8217 (pt0) REVERT: G 132 PHE cc_start: 0.8643 (t80) cc_final: 0.8410 (t80) outliers start: 14 outliers final: 2 residues processed: 122 average time/residue: 0.4943 time to fit residues: 65.1103 Evaluate side-chains 97 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 82 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [84, 89, 96, 31, 58, 49, 47, 102, 99, 77, 87] chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.161510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126292 restraints weight = 11062.434| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.25 r_work: 0.3678 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9359 Z= 0.116 Angle : 0.486 9.390 12355 Z= 0.238 Chirality : 0.041 0.122 1470 Planarity : 0.003 0.027 1379 Dihedral : 15.210 160.195 1890 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.07 % Allowed : 10.87 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.25), residues: 1085 helix: 2.75 (0.18), residues: 721 sheet: -0.36 (0.48), residues: 105 loop : -1.28 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.019 0.001 TYR E 56 PHE 0.013 0.001 PHE C 87 TRP 0.003 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9359) covalent geometry : angle 0.48581 / 0.24 (12355) hydrogen bonds : bond 0.03922 / 2.64 ( 658) hydrogen bonds : angle 3.55206 / 2.57 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.277 Fit side-chains REVERT: B 132 PHE cc_start: 0.8695 (t80) cc_final: 0.8275 (t80) REVERT: B 144 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: C 82 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8194 (mp) REVERT: C 159 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7817 (mtp85) REVERT: D 132 PHE cc_start: 0.8788 (t80) cc_final: 0.8563 (t80) REVERT: D 144 GLU cc_start: 0.8196 (tt0) cc_final: 0.7928 (tm-30) REVERT: E 116 GLU cc_start: 0.8510 (pt0) cc_final: 0.8222 (pt0) REVERT: G 30 LYS cc_start: 0.7558 (mmmt) cc_final: 0.7152 (mtmm) REVERT: G 116 GLU cc_start: 0.8461 (pt0) cc_final: 0.8198 (pt0) REVERT: G 132 PHE cc_start: 0.8699 (t80) cc_final: 0.8426 (t80) outliers start: 10 outliers final: 3 residues processed: 122 average time/residue: 0.4600 time to fit residues: 60.8422 Evaluate side-chains 104 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 82 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [19, 94, 82, 88, 42, 99, 76, 14, 57, 33, 85] chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 82 optimal weight: 0.4980 chunk 88 optimal weight: 0.1980 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.163594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127588 restraints weight = 11071.826| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.27 r_work: 0.3699 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 9359 Z= 0.099 Angle : 0.469 11.255 12355 Z= 0.227 Chirality : 0.040 0.123 1470 Planarity : 0.003 0.028 1379 Dihedral : 15.035 161.273 1890 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.96 % Allowed : 11.73 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.25), residues: 1085 helix: 2.90 (0.18), residues: 721 sheet: -0.14 (0.48), residues: 105 loop : -1.19 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.018 0.001 TYR E 56 PHE 0.009 0.001 PHE E 132 TRP 0.004 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 ( 9359) covalent geometry : angle 0.46883 / 0.23 (12355) hydrogen bonds : bond 0.03645 / 2.45 ( 658) hydrogen bonds : angle 3.47296 / 2.51 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.284 Fit side-chains REVERT: B 132 PHE cc_start: 0.8688 (t80) cc_final: 0.8283 (t80) REVERT: B 144 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: C 159 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7823 (mtp85) REVERT: D 144 GLU cc_start: 0.8115 (tt0) cc_final: 0.7888 (tm-30) REVERT: E 116 GLU cc_start: 0.8494 (pt0) cc_final: 0.8231 (pt0) REVERT: E 132 PHE cc_start: 0.8506 (t80) cc_final: 0.7775 (t80) REVERT: F 124 LYS cc_start: 0.8400 (mmtp) cc_final: 0.7748 (mmmt) REVERT: F 132 PHE cc_start: 0.8444 (t80) cc_final: 0.7788 (t80) REVERT: G 30 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7334 (mtmm) REVERT: G 116 GLU cc_start: 0.8441 (pt0) cc_final: 0.8173 (pt0) REVERT: G 132 PHE cc_start: 0.8653 (t80) cc_final: 0.8337 (t80) outliers start: 9 outliers final: 2 residues processed: 122 average time/residue: 0.4729 time to fit residues: 62.2776 Evaluate side-chains 104 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain F residue 82 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [4, 58, 70, 55, 34, 99, 88, 43, 44, 39, 51] chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 55 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.162034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125965 restraints weight = 11118.256| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.25 r_work: 0.3679 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9359 Z= 0.116 Angle : 0.524 12.662 12355 Z= 0.247 Chirality : 0.041 0.121 1470 Planarity : 0.003 0.028 1379 Dihedral : 15.087 160.668 1890 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.07 % Allowed : 12.90 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.25), residues: 1085 helix: 2.84 (0.18), residues: 721 sheet: -0.16 (0.48), residues: 105 loop : -1.09 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.020 0.001 TYR A 56 PHE 0.007 0.001 PHE C 87 TRP 0.003 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 9359) covalent geometry : angle 0.52369 / 0.25 (12355) hydrogen bonds : bond 0.03822 / 2.57 ( 658) hydrogen bonds : angle 3.50567 / 2.54 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.353 Fit side-chains REVERT: B 132 PHE cc_start: 0.8742 (t80) cc_final: 0.8359 (t80) REVERT: B 144 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: C 82 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8185 (mp) REVERT: C 124 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8020 (mtpt) REVERT: C 132 PHE cc_start: 0.8089 (t80) cc_final: 0.7845 (t80) REVERT: C 159 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7856 (mtp85) REVERT: E 116 GLU cc_start: 0.8528 (pt0) cc_final: 0.8247 (pt0) REVERT: E 128 LYS cc_start: 0.8311 (mtmm) cc_final: 0.8062 (mtmm) REVERT: E 132 PHE cc_start: 0.8575 (t80) cc_final: 0.8300 (t80) REVERT: F 124 LYS cc_start: 0.8382 (mmtp) cc_final: 0.7749 (mmmt) REVERT: F 132 PHE cc_start: 0.8484 (t80) cc_final: 0.7740 (t80) REVERT: G 30 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7213 (mtmm) REVERT: G 116 GLU cc_start: 0.8467 (pt0) cc_final: 0.8183 (pt0) REVERT: G 132 PHE cc_start: 0.8729 (t80) cc_final: 0.8452 (t80) outliers start: 10 outliers final: 2 residues processed: 118 average time/residue: 0.5331 time to fit residues: 67.4506 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain F residue 82 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [42, 49, 61, 40, 60, 31, 66, 59, 96, 51, 46] chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 96 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113842 restraints weight = 10292.074| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.34 r_work: 0.3280 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9359 Z= 0.167 Angle : 0.586 11.249 12355 Z= 0.281 Chirality : 0.043 0.147 1470 Planarity : 0.003 0.029 1379 Dihedral : 15.508 159.095 1890 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.75 % Allowed : 14.50 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.25), residues: 1085 helix: 2.59 (0.18), residues: 721 sheet: -0.27 (0.47), residues: 105 loop : -1.14 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 159 TYR 0.023 0.002 TYR A 56 PHE 0.007 0.001 PHE E 59 TRP 0.003 0.001 TRP E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 9359) covalent geometry : angle 0.58628 / 0.28 (12355) hydrogen bonds : bond 0.04341 / 2.92 ( 658) hydrogen bonds : angle 3.64483 / 2.66 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.354 Fit side-chains REVERT: A 113 GLU cc_start: 0.7977 (pt0) cc_final: 0.7665 (pt0) REVERT: B 49 GLN cc_start: 0.6759 (mt0) cc_final: 0.6556 (mt0) REVERT: B 132 PHE cc_start: 0.8674 (t80) cc_final: 0.8295 (t80) REVERT: B 144 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: C 82 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8238 (mp) REVERT: C 159 ARG cc_start: 0.8075 (mtp-110) cc_final: 0.7808 (mtp85) REVERT: D 144 GLU cc_start: 0.7993 (tt0) cc_final: 0.7761 (tm-30) REVERT: E 116 GLU cc_start: 0.8519 (pt0) cc_final: 0.8218 (pt0) REVERT: F 116 GLU cc_start: 0.8543 (pt0) cc_final: 0.8210 (pt0) REVERT: F 124 LYS cc_start: 0.8377 (mmtp) cc_final: 0.7784 (mtpt) REVERT: F 132 PHE cc_start: 0.8686 (t80) cc_final: 0.8392 (t80) REVERT: G 30 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7247 (mtmm) REVERT: G 116 GLU cc_start: 0.8442 (pt0) cc_final: 0.8094 (pt0) REVERT: G 132 PHE cc_start: 0.8636 (t80) cc_final: 0.8392 (t80) outliers start: 7 outliers final: 1 residues processed: 115 average time/residue: 0.5443 time to fit residues: 67.1279 Evaluate side-chains 105 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain F residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [10, 54, 71, 68, 87, 9, 35, 60, 83, 82, 84] chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.160589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124803 restraints weight = 11033.594| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.23 r_work: 0.3678 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9359 Z= 0.123 Angle : 0.519 10.462 12355 Z= 0.249 Chirality : 0.041 0.119 1470 Planarity : 0.003 0.030 1379 Dihedral : 15.285 159.937 1890 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.96 % Allowed : 14.61 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.25), residues: 1085 helix: 2.73 (0.18), residues: 721 sheet: -0.17 (0.48), residues: 105 loop : -1.08 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 159 TYR 0.020 0.001 TYR A 56 PHE 0.007 0.001 PHE D 120 TRP 0.004 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9359) covalent geometry : angle 0.51872 / 0.25 (12355) hydrogen bonds : bond 0.03907 / 2.63 ( 658) hydrogen bonds : angle 3.52927 / 2.56 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.353 Fit side-chains REVERT: A 113 GLU cc_start: 0.8115 (pt0) cc_final: 0.7818 (pt0) REVERT: B 132 PHE cc_start: 0.8828 (t80) cc_final: 0.8539 (t80) REVERT: B 144 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: C 82 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8550 (mp) REVERT: C 159 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.8096 (mtp85) REVERT: E 116 GLU cc_start: 0.8588 (pt0) cc_final: 0.8346 (pt0) REVERT: F 116 GLU cc_start: 0.8624 (pt0) cc_final: 0.8333 (pt0) REVERT: F 124 LYS cc_start: 0.8457 (mmtp) cc_final: 0.7942 (mtpt) REVERT: F 132 PHE cc_start: 0.8763 (t80) cc_final: 0.8545 (t80) REVERT: G 30 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7615 (mtmm) REVERT: G 116 GLU cc_start: 0.8525 (pt0) cc_final: 0.8240 (pt0) outliers start: 9 outliers final: 2 residues processed: 120 average time/residue: 0.5295 time to fit residues: 68.3161 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain F residue 82 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [28, 45, 69, 40, 26, 31, 43, 68, 18, 91, 41] chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113738 restraints weight = 10207.252| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.32 r_work: 0.3287 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9359 Z= 0.168 Angle : 0.598 13.918 12355 Z= 0.286 Chirality : 0.043 0.149 1470 Planarity : 0.003 0.031 1379 Dihedral : 15.598 158.744 1890 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.96 % Allowed : 15.14 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.25), residues: 1085 helix: 2.52 (0.18), residues: 721 sheet: -0.26 (0.48), residues: 105 loop : -1.04 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 159 TYR 0.023 0.002 TYR A 56 PHE 0.009 0.001 PHE E 59 TRP 0.005 0.001 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 9359) covalent geometry : angle 0.59814 / 0.29 (12355) hydrogen bonds : bond 0.04321 / 2.91 ( 658) hydrogen bonds : angle 3.63023 / 2.65 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.336 Fit side-chains REVERT: B 49 GLN cc_start: 0.6840 (mt0) cc_final: 0.6635 (mt0) REVERT: B 132 PHE cc_start: 0.8690 (t80) cc_final: 0.8324 (t80) REVERT: B 144 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: C 82 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8229 (mp) REVERT: C 132 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7476 (t80) REVERT: C 159 ARG cc_start: 0.8109 (mtp-110) cc_final: 0.7857 (mtp85) REVERT: D 144 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: E 116 GLU cc_start: 0.8511 (pt0) cc_final: 0.8212 (pt0) REVERT: F 116 GLU cc_start: 0.8517 (pt0) cc_final: 0.8183 (pt0) REVERT: F 124 LYS cc_start: 0.8385 (mmtp) cc_final: 0.7814 (mtpt) REVERT: G 30 LYS cc_start: 0.7653 (mmmt) cc_final: 0.7295 (mtmm) REVERT: G 116 GLU cc_start: 0.8438 (pt0) cc_final: 0.8188 (pt0) outliers start: 9 outliers final: 3 residues processed: 109 average time/residue: 0.5491 time to fit residues: 64.2038 Evaluate side-chains 109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [9, 87, 44, 47, 89, 3, 70, 12, 98, 48, 26] chunk 9 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115144 restraints weight = 10258.471| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.34 r_work: 0.3307 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.003 0.031 9359 Z= 0.134 Angle : 0.560 12.618 12355 Z= 0.266 Chirality : 0.042 0.120 1470 Planarity : 0.003 0.031 1379 Dihedral : 15.397 159.310 1890 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.85 % Allowed : 15.46 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.25), residues: 1085 helix: 2.65 (0.18), residues: 721 sheet: -0.13 (0.49), residues: 105 loop : -0.97 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 159 TYR 0.020 0.002 TYR C 56 PHE 0.007 0.001 PHE D 120 TRP 0.006 0.001 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9359) covalent geometry : angle 0.56000 / 0.27 (12355) hydrogen bonds : bond 0.03992 / 2.69 ( 658) hydrogen bonds : angle 3.55476 / 2.59 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.396 Fit side-chains REVERT: B 132 PHE cc_start: 0.8630 (t80) cc_final: 0.8250 (t80) REVERT: B 144 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: C 82 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 132 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7414 (t80) REVERT: C 159 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7841 (mtp85) REVERT: D 144 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: E 116 GLU cc_start: 0.8518 (pt0) cc_final: 0.8228 (pt0) REVERT: E 132 PHE cc_start: 0.8660 (t80) cc_final: 0.8318 (t80) REVERT: F 116 GLU cc_start: 0.8508 (pt0) cc_final: 0.8180 (pt0) REVERT: F 124 LYS cc_start: 0.8372 (mmtp) cc_final: 0.7793 (mtpt) REVERT: G 30 LYS cc_start: 0.7682 (mmmt) cc_final: 0.7322 (mtmm) REVERT: G 116 GLU cc_start: 0.8414 (pt0) cc_final: 0.8189 (pt0) outliers start: 8 outliers final: 2 residues processed: 115 average time/residue: 0.5558 time to fit residues: 68.3707 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain F residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [69, 3, 79, 51, 47, 57, 19, 31, 95, 56, 24] chunk 69 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.151630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115711 restraints weight = 10164.309| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.32 r_work: 0.3316 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9359 Z= 0.128 Angle : 0.557 11.279 12355 Z= 0.267 Chirality : 0.042 0.119 1470 Planarity : 0.003 0.029 1379 Dihedral : 15.290 159.682 1890 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.96 % Allowed : 15.14 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.26), residues: 1085 helix: 2.69 (0.18), residues: 721 sheet: -0.11 (0.50), residues: 105 loop : -0.90 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 159 TYR 0.020 0.002 TYR C 56 PHE 0.007 0.001 PHE D 120 TRP 0.008 0.001 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9359) covalent geometry : angle 0.55715 / 0.27 (12355) hydrogen bonds : bond 0.03904 / 2.63 ( 658) hydrogen bonds : angle 3.54469 / 2.58 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.75 seconds wall clock time: 53 minutes 49.91 seconds (3229.91 seconds total)