Starting phenix.real_space_refine on Fri Oct 23 07:47:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sdo_54788/10_2026/9sdo_54788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sdo_54788/10_2026/9sdo_54788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sdo_54788/10_2026/9sdo_54788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sdo_54788/10_2026/9sdo_54788.map" model { file = "/net/cci-nas-00/data/ceres_data/9sdo_54788/10_2026/9sdo_54788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sdo_54788/10_2026/9sdo_54788.cif" } resolution = 2.9 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= 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 21 5.16 5 C 6179 2.51 5 N 1274 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 9042 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 105 Unusual residues: {'C14': 2, 'D10': 1, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 58 Unusual residues: {'C14': 3, 'OCT': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'C14': 4, 'D10': 2, 'D12': 2, 'OCT': 1, 'PEE': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 113 Unusual residues: {'C14': 2, 'D10': 2, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "E" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 99 Unusual residues: {'C14': 3, 'D10': 1, 'OCT': 1, 'PEE': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "F" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 132 Unusual residues: {'C14': 2, 'D12': 1, 'OCT': 2, 'PEE': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "G" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'D10': 1, 'D12': 2, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 1.21, per 1000 atoms: 0.13 Number of scatterers: 9042 At special positions: 0 Unit cell: (86.086, 85.14, 97.438, 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 6179 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: 0.53 Conformation dependent library (CDL) restraints added in 167.6 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 12 sheets defined 65.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 7 through 40 removed outlier: 4.019A 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: 3.670A 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 42 removed outlier: 4.295A pdb=" N PHE B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 72 Processing helix chain 'B' and resid 75 through 91 Processing helix chain 'B' and resid 93 through 109 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'C' and resid 7 through 40 removed outlier: 3.773A 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 91 Processing helix chain 'C' and resid 93 through 109 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'D' and resid 8 through 41 Processing helix chain 'D' and resid 44 through 72 Processing helix chain 'D' and resid 75 through 93 Processing helix chain 'D' and resid 94 through 109 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'E' and resid 8 through 40 Processing helix chain 'E' and resid 45 through 72 Processing helix chain 'E' and resid 75 through 93 removed outlier: 4.165A pdb=" N LEU E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 109 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'F' and resid 7 through 40 removed outlier: 3.927A pdb=" N PHE F 11 " --> pdb=" O ASN F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 72 Processing helix chain 'F' and resid 75 through 91 Processing helix chain 'F' and resid 93 through 109 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'G' and resid 7 through 40 removed outlier: 4.048A 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 91 Processing helix chain 'G' and resid 93 through 109 Processing helix chain 'G' and resid 149 through 153 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 119 removed outlier: 6.622A pdb=" N LYS A 136 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE A 130 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.576A pdb=" N SER B 129 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.715A pdb=" N GLY B 125 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.589A pdb=" N SER C 129 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.743A pdb=" N GLY C 125 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 156 through 159 removed outlier: 3.635A pdb=" N ILE D 145 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 129 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.604A pdb=" N GLY D 125 " --> pdb=" O VAL D 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 157 through 159 removed outlier: 3.638A pdb=" N ILE E 145 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 129 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 117 through 119 Processing sheet with id=AB1, first strand: chain 'E' and resid 157 through 159 removed outlier: 3.651A pdb=" N ILE F 145 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE F 130 " --> pdb=" O TYR F 134 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS F 136 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY F 125 " --> pdb=" O VAL F 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 157 through 159 Processing sheet with id=AB3, first strand: chain 'G' and resid 117 through 119 removed outlier: 3.626A pdb=" N GLY G 125 " --> pdb=" O VAL G 118 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1863 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: 1.36 Time building geometry restraints manager: 0.62 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: 1319 1.32 - 1.44: 2136 1.44 - 1.56: 5631 1.56 - 1.68: 14 1.68 - 1.80: 35 Bond restraints: 9135 Sorted by residual: bond pdb=" C38 PEE D 201 " pdb=" C39 PEE D 201 " ideal model delta sigma weight residual 1.523 1.316 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C38 PEE F 201 " pdb=" C39 PEE F 201 " ideal model delta sigma weight residual 1.523 1.316 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C18 PEE E 201 " pdb=" C19 PEE E 201 " ideal model delta sigma weight residual 1.523 1.317 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C18 PEE A 203 " pdb=" C19 PEE A 203 " ideal model delta sigma weight residual 1.523 1.317 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C38 PEE G 201 " pdb=" C39 PEE G 201 " ideal model delta sigma weight residual 1.523 1.317 0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 9130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 12044 3.07 - 6.13: 75 6.13 - 9.20: 15 9.20 - 12.27: 3 12.27 - 15.34: 17 Bond angle restraints: 12154 Sorted by residual: angle pdb=" C38 PEE A 203 " pdb=" C39 PEE A 203 " pdb=" C40 PEE A 203 " ideal model delta sigma weight residual 112.47 127.81 -15.34 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C38 PEE E 201 " pdb=" C39 PEE E 201 " pdb=" C40 PEE E 201 " ideal model delta sigma weight residual 112.47 127.26 -14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C38 PEE F 201 " pdb=" C39 PEE F 201 " pdb=" C40 PEE F 201 " ideal model delta sigma weight residual 112.47 126.92 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C38 PEE C 201 " pdb=" C39 PEE C 201 " pdb=" C40 PEE C 201 " ideal model delta sigma weight residual 112.47 126.72 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C38 PEE G 201 " pdb=" C39 PEE G 201 " pdb=" C40 PEE G 201 " ideal model delta sigma weight residual 112.47 126.43 -13.96 3.00e+00 1.11e-01 2.17e+01 ... (remaining 12149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 5389 35.83 - 71.66: 89 71.66 - 107.48: 16 107.48 - 143.31: 5 143.31 - 179.14: 14 Dihedral angle restraints: 5513 sinusoidal: 2377 harmonic: 3136 Sorted by residual: dihedral pdb=" C2 PEE F 201 " pdb=" C10 PEE F 201 " pdb=" O2 PEE F 201 " pdb=" O4 PEE F 201 " ideal model delta sinusoidal sigma weight residual 2.73 -176.41 179.14 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C2 PEE G 201 " pdb=" C10 PEE G 201 " pdb=" O2 PEE G 201 " pdb=" O4 PEE G 201 " ideal model delta sinusoidal sigma weight residual 2.73 174.09 -171.36 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C2 PEE D 201 " pdb=" C10 PEE D 201 " pdb=" O2 PEE D 201 " pdb=" O4 PEE D 201 " ideal model delta sinusoidal sigma weight residual 2.73 173.94 -171.21 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1281 0.060 - 0.120: 170 0.120 - 0.180: 12 0.180 - 0.241: 1 0.241 - 0.301: 6 Chirality restraints: 1470 Sorted by residual: chirality pdb=" C2 PEE D 201 " pdb=" C1 PEE D 201 " pdb=" C3 PEE D 201 " pdb=" O2 PEE D 201 " both_signs ideal model delta sigma weight residual False -2.33 -2.63 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C2 PEE A 203 " pdb=" C1 PEE A 203 " pdb=" C3 PEE A 203 " pdb=" O2 PEE A 203 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C2 PEE G 201 " pdb=" C1 PEE G 201 " pdb=" C3 PEE G 201 " pdb=" O2 PEE G 201 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1467 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 28 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ALA B 28 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA B 28 " 0.009 2.00e-02 2.50e+03 pdb=" N SER B 29 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 42 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" CD GLU C 42 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU C 42 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 42 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PEE F 205 " -0.022 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C11 PEE F 205 " 0.006 2.00e-02 2.50e+03 pdb=" O2 PEE F 205 " 0.007 2.00e-02 2.50e+03 pdb=" O4 PEE F 205 " 0.009 2.00e-02 2.50e+03 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1622 2.77 - 3.30: 8569 3.30 - 3.83: 14355 3.83 - 4.37: 16922 4.37 - 4.90: 30185 Nonbonded interactions: 71653 Sorted by model distance: nonbonded pdb=" O GLY E 80 " pdb=" OG1 THR E 83 " model vdw 2.237 3.040 nonbonded pdb=" OG SER B 148 " pdb=" OD1 ASN B 150 " model vdw 2.255 3.040 nonbonded pdb=" OG SER F 148 " pdb=" OD1 ASN F 150 " model vdw 2.269 3.040 nonbonded pdb=" O SER E 109 " pdb=" OG SER E 109 " model vdw 2.320 3.040 nonbonded pdb=" O SER C 109 " pdb=" OG SER C 109 " model vdw 2.346 3.040 ... (remaining 71648 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: 0.240 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.540 Find NCS groups from input model: 0.230 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:4.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.010 0.207 9135 Z= 0.461 Angle : 0.818 15.337 12154 Z= 0.351 Chirality : 0.045 0.301 1470 Planarity : 0.003 0.027 1379 Dihedral : 18.092 179.141 3511 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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 (0.26), residues: 1085 helix: 2.87 (0.18), residues: 721 sheet: -1.57 (0.49), residues: 105 loop : -1.42 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 159 TYR 0.016 0.002 TYR C 56 PHE 0.009 0.001 PHE G 11 TRP 0.004 0.001 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.46 ( 9135) covalent geometry : angle 0.81765 / 0.35 (12154) hydrogen bonds : bond 0.10820 / 7.18 ( 634) hydrogen bonds : angle 4.91390 / 3.58 ( 1863) *********************** 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 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.201 Fit side-chains REVERT: B 41 LYS cc_start: 0.7442 (ttpp) cc_final: 0.7186 (ttpp) REVERT: D 59 PHE cc_start: 0.8082 (t80) cc_final: 0.7866 (t80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3322 time to fit residues: 46.0538 Evaluate side-chains 104 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.116047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.091133 restraints weight = 11051.213| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.94 r_work: 0.2829 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9135 Z= 0.133 Angle : 0.478 7.843 12154 Z= 0.243 Chirality : 0.040 0.136 1470 Planarity : 0.003 0.023 1379 Dihedral : 16.770 158.469 1712 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.03 % Allowed : 6.18 % Favored : 91.79 % 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: 2.74 (0.26), residues: 1085 helix: 3.25 (0.18), residues: 728 sheet: -0.83 (0.51), residues: 105 loop : -1.55 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 159 TYR 0.017 0.001 TYR E 37 PHE 0.013 0.001 PHE E 11 TRP 0.002 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9135) covalent geometry : angle 0.47782 / 0.24 (12154) hydrogen bonds : bond 0.04527 / 3.13 ( 634) hydrogen bonds : angle 3.51270 / 2.57 ( 1863) *********************** 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 133 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.295 Fit side-chains REVERT: A 113 GLU cc_start: 0.8425 (pm20) cc_final: 0.8094 (pm20) REVERT: A 116 GLU cc_start: 0.8327 (pt0) cc_final: 0.8048 (pt0) REVERT: C 40 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6862 (mp) REVERT: E 119 ASP cc_start: 0.8461 (t70) cc_final: 0.8216 (t0) REVERT: F 113 GLU cc_start: 0.8673 (tt0) cc_final: 0.7996 (tp30) REVERT: F 151 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8706 (mp) REVERT: G 117 LYS cc_start: 0.8542 (mttt) cc_final: 0.8153 (mtpp) outliers start: 19 outliers final: 6 residues processed: 124 average time/residue: 0.5135 time to fit residues: 68.3609 Evaluate side-chains 108 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [71, 87, 42, 21, 88, 20, 31, 61, 50, 12, 46] chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.113143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.088368 restraints weight = 11208.965| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.94 r_work: 0.2799 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9135 Z= 0.170 Angle : 0.499 8.889 12154 Z= 0.251 Chirality : 0.041 0.135 1470 Planarity : 0.003 0.023 1379 Dihedral : 15.417 154.735 1712 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.56 % Allowed : 9.28 % Favored : 88.17 % 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: 2.70 (0.26), residues: 1085 helix: 3.15 (0.17), residues: 728 sheet: -0.39 (0.53), residues: 105 loop : -1.57 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.020 0.002 TYR D 37 PHE 0.009 0.001 PHE E 11 TRP 0.003 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 9135) covalent geometry : angle 0.49923 / 0.25 (12154) hydrogen bonds : bond 0.04850 / 3.36 ( 634) hydrogen bonds : angle 3.42483 / 2.52 ( 1863) *********************** 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 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.333 Fit side-chains REVERT: A 113 GLU cc_start: 0.8403 (pm20) cc_final: 0.8063 (pm20) REVERT: A 116 GLU cc_start: 0.8384 (pt0) cc_final: 0.8115 (pt0) REVERT: C 40 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6895 (mp) REVERT: F 113 GLU cc_start: 0.8657 (tt0) cc_final: 0.8018 (tp30) outliers start: 24 outliers final: 8 residues processed: 113 average time/residue: 0.4675 time to fit residues: 57.1678 Evaluate side-chains 109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [26, 33, 74, 102, 50, 79, 88, 44, 100, 89, 68] chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.111310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.086638 restraints weight = 11385.268| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.96 r_work: 0.2770 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9135 Z= 0.208 Angle : 0.531 10.317 12154 Z= 0.267 Chirality : 0.042 0.136 1470 Planarity : 0.003 0.026 1379 Dihedral : 15.314 157.028 1712 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.99 % Allowed : 10.55 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.52 (0.25), residues: 1085 helix: 2.99 (0.17), residues: 728 sheet: -0.27 (0.53), residues: 105 loop : -1.66 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 159 TYR 0.020 0.002 TYR E 37 PHE 0.009 0.001 PHE E 11 TRP 0.005 0.001 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 ( 9135) covalent geometry : angle 0.53053 / 0.27 (12154) hydrogen bonds : bond 0.05156 / 3.57 ( 634) hydrogen bonds : angle 3.47560 / 2.55 ( 1863) *********************** 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 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.314 Fit side-chains REVERT: A 113 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7990 (pm20) REVERT: A 116 GLU cc_start: 0.8351 (pt0) cc_final: 0.8075 (pt0) REVERT: C 40 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6932 (mp) REVERT: E 119 ASP cc_start: 0.8554 (t70) cc_final: 0.8304 (t0) REVERT: F 113 GLU cc_start: 0.8609 (tt0) cc_final: 0.7919 (tp30) outliers start: 28 outliers final: 12 residues processed: 117 average time/residue: 0.4710 time to fit residues: 59.5982 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [7, 72, 88, 100, 41, 48, 32, 70, 21, 71, 90] chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.116736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092074 restraints weight = 11112.819| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.94 r_work: 0.2930 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9135 Z= 0.104 Angle : 0.425 8.159 12154 Z= 0.215 Chirality : 0.039 0.127 1470 Planarity : 0.002 0.021 1379 Dihedral : 13.816 151.474 1712 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.24 % Allowed : 11.83 % Favored : 85.93 % 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: 3.03 (0.26), residues: 1085 helix: 3.38 (0.18), residues: 728 sheet: -0.00 (0.54), residues: 105 loop : -1.49 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 159 TYR 0.017 0.001 TYR E 37 PHE 0.007 0.001 PHE E 11 TRP 0.005 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 9135) covalent geometry : angle 0.42466 / 0.21 (12154) hydrogen bonds : bond 0.03884 / 2.69 ( 634) hydrogen bonds : angle 3.11000 / 2.29 ( 1863) *********************** 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 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.325 Fit side-chains REVERT: A 113 GLU cc_start: 0.8421 (pm20) cc_final: 0.8092 (pm20) REVERT: A 116 GLU cc_start: 0.8388 (pt0) cc_final: 0.8158 (pt0) REVERT: C 40 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6950 (mp) REVERT: C 132 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8771 (t80) REVERT: F 113 GLU cc_start: 0.8645 (tt0) cc_final: 0.8112 (tp30) outliers start: 21 outliers final: 10 residues processed: 112 average time/residue: 0.4608 time to fit residues: 55.9061 Evaluate side-chains 109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 82 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [91, 92, 19, 15, 31, 82, 71, 97, 14, 89, 100] chunk 91 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.113201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.088399 restraints weight = 11166.494| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.95 r_work: 0.2815 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9135 Z= 0.158 Angle : 0.484 9.143 12154 Z= 0.241 Chirality : 0.040 0.131 1470 Planarity : 0.002 0.020 1379 Dihedral : 13.990 152.272 1712 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.77 % Allowed : 12.47 % 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: 2.85 (0.26), residues: 1085 helix: 3.23 (0.17), residues: 728 sheet: -0.10 (0.53), residues: 105 loop : -1.51 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.019 0.001 TYR A 37 PHE 0.007 0.001 PHE E 11 TRP 0.004 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 9135) covalent geometry : angle 0.48367 / 0.24 (12154) hydrogen bonds : bond 0.04569 / 3.17 ( 634) hydrogen bonds : angle 3.25355 / 2.39 ( 1863) *********************** 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 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.261 Fit side-chains REVERT: A 113 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: A 116 GLU cc_start: 0.8421 (pt0) cc_final: 0.8141 (pt0) REVERT: C 40 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6950 (mp) REVERT: C 132 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8844 (t80) REVERT: F 113 GLU cc_start: 0.8624 (tt0) cc_final: 0.8066 (tp30) REVERT: G 128 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8578 (ttmm) outliers start: 26 outliers final: 12 residues processed: 117 average time/residue: 0.4652 time to fit residues: 58.6848 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 128 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [65, 53, 62, 73, 39, 21, 72, 83, 66, 78, 92] chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.116691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.092339 restraints weight = 11124.526| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.88 r_work: 0.2906 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9135 Z= 0.109 Angle : 0.433 8.401 12154 Z= 0.218 Chirality : 0.039 0.129 1470 Planarity : 0.002 0.019 1379 Dihedral : 13.320 150.814 1712 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.24 % Allowed : 13.54 % Favored : 84.22 % 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: 3.06 (0.26), residues: 1085 helix: 3.38 (0.17), residues: 728 sheet: 0.00 (0.53), residues: 105 loop : -1.41 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 159 TYR 0.016 0.001 TYR E 37 PHE 0.007 0.001 PHE G 87 TRP 0.004 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9135) covalent geometry : angle 0.43280 / 0.22 (12154) hydrogen bonds : bond 0.03932 / 2.72 ( 634) hydrogen bonds : angle 3.09571 / 2.28 ( 1863) *********************** 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 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.324 Fit side-chains REVERT: A 113 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: A 116 GLU cc_start: 0.8403 (pt0) cc_final: 0.8173 (pt0) REVERT: C 40 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6926 (mp) REVERT: C 132 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8783 (t80) REVERT: E 75 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8100 (pp) REVERT: F 113 GLU cc_start: 0.8594 (tt0) cc_final: 0.8060 (tp30) REVERT: G 128 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8722 (ttmm) outliers start: 21 outliers final: 10 residues processed: 112 average time/residue: 0.4685 time to fit residues: 56.8397 Evaluate side-chains 113 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain G residue 128 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [8, 31, 23, 68, 38, 86, 5, 10, 81, 56, 28] chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 28 optimal weight: 6.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.118127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.093542 restraints weight = 11056.150| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.93 r_work: 0.2965 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9135 Z= 0.099 Angle : 0.438 8.525 12154 Z= 0.219 Chirality : 0.039 0.127 1470 Planarity : 0.002 0.018 1379 Dihedral : 12.838 150.399 1712 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.56 % Allowed : 13.11 % Favored : 84.33 % 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: 3.20 (0.26), residues: 1085 helix: 3.51 (0.17), residues: 721 sheet: 0.02 (0.53), residues: 105 loop : -1.25 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 159 TYR 0.017 0.001 TYR A 37 PHE 0.012 0.001 PHE A 87 TRP 0.004 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 9135) covalent geometry : angle 0.43794 / 0.22 (12154) hydrogen bonds : bond 0.03691 / 2.56 ( 634) hydrogen bonds : angle 3.00356 / 2.21 ( 1863) *********************** 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 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.307 Fit side-chains REVERT: A 113 GLU cc_start: 0.8360 (pm20) cc_final: 0.7976 (pm20) REVERT: A 116 GLU cc_start: 0.8364 (pt0) cc_final: 0.8096 (pt0) REVERT: C 40 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6854 (mp) REVERT: C 132 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8814 (t80) REVERT: E 75 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8158 (pp) REVERT: F 113 GLU cc_start: 0.8619 (tt0) cc_final: 0.8087 (tp30) REVERT: G 128 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8689 (ttmm) outliers start: 24 outliers final: 11 residues processed: 115 average time/residue: 0.4963 time to fit residues: 61.4789 Evaluate side-chains 106 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain G residue 128 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [96, 75, 89, 4, 29, 82, 100, 0, 97, 16, 85] chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.114293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.089665 restraints weight = 11117.161| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.94 r_work: 0.2887 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9135 Z= 0.139 Angle : 0.480 9.384 12154 Z= 0.240 Chirality : 0.040 0.131 1470 Planarity : 0.002 0.019 1379 Dihedral : 13.066 150.757 1712 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.03 % Allowed : 13.43 % Favored : 84.54 % 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: 2.95 (0.26), residues: 1085 helix: 3.29 (0.17), residues: 728 sheet: -0.05 (0.52), residues: 105 loop : -1.44 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 159 TYR 0.014 0.001 TYR C 56 PHE 0.006 0.001 PHE E 11 TRP 0.004 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9135) covalent geometry : angle 0.48019 / 0.24 (12154) hydrogen bonds : bond 0.04332 / 3.00 ( 634) hydrogen bonds : angle 3.17081 / 2.33 ( 1863) *********************** 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 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.333 Fit side-chains REVERT: A 113 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: A 116 GLU cc_start: 0.8424 (pt0) cc_final: 0.8182 (pt0) REVERT: C 40 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6851 (mp) REVERT: C 132 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8876 (t80) REVERT: E 37 TYR cc_start: 0.6923 (t80) cc_final: 0.6172 (t80) REVERT: E 75 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8150 (pp) REVERT: F 113 GLU cc_start: 0.8575 (tt0) cc_final: 0.8026 (tp30) REVERT: G 128 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8639 (ttmm) outliers start: 19 outliers final: 9 residues processed: 109 average time/residue: 0.4882 time to fit residues: 57.4534 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain G residue 128 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [63, 22, 91, 80, 78, 68, 39, 6, 76, 36, 54] chunk 63 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 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 = 0.3275 r_free = 0.3275 target = 0.112958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.088501 restraints weight = 11225.876| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.93 r_work: 0.2897 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9135 Z= 0.160 Angle : 0.510 10.226 12154 Z= 0.253 Chirality : 0.041 0.134 1470 Planarity : 0.002 0.019 1379 Dihedral : 13.095 150.073 1712 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.24 % Allowed : 13.22 % Favored : 84.54 % 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: 2.83 (0.26), residues: 1085 helix: 3.21 (0.17), residues: 728 sheet: -0.08 (0.51), residues: 105 loop : -1.50 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 159 TYR 0.019 0.001 TYR A 37 PHE 0.008 0.001 PHE G 11 TRP 0.005 0.001 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 9135) covalent geometry : angle 0.50980 / 0.25 (12154) hydrogen bonds : bond 0.04562 / 3.15 ( 634) hydrogen bonds : angle 3.22704 / 2.37 ( 1863) ********************** 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 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.332 Fit side-chains REVERT: A 113 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: A 116 GLU cc_start: 0.8427 (pt0) cc_final: 0.8184 (pt0) REVERT: C 40 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6897 (mp) REVERT: C 132 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8848 (t80) REVERT: E 37 TYR cc_start: 0.6880 (t80) cc_final: 0.6068 (t80) REVERT: E 75 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8127 (pp) REVERT: F 113 GLU cc_start: 0.8611 (tt0) cc_final: 0.8055 (tp30) REVERT: G 128 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8576 (ttmm) outliers start: 21 outliers final: 12 residues processed: 113 average time/residue: 0.4719 time to fit residues: 57.7104 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 128 LYS Chi-restraints excluded: chain G residue 139 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [25, 30, 2, 3, 27, 64, 69, 50, 12, 61, 55] chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.114927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.090398 restraints weight = 11078.884| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.93 r_work: 0.2845 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9135 Z= 0.126 Angle : 0.469 9.224 12154 Z= 0.236 Chirality : 0.040 0.127 1470 Planarity : 0.002 0.019 1379 Dihedral : 12.583 148.079 1712 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.92 % Allowed : 13.33 % 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: 2.93 (0.26), residues: 1085 helix: 3.29 (0.17), residues: 728 sheet: -0.05 (0.52), residues: 105 loop : -1.48 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 159 TYR 0.014 0.001 TYR E 97 PHE 0.006 0.001 PHE E 11 TRP 0.005 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9135) covalent geometry : angle 0.46882 / 0.24 (12154) hydrogen bonds : bond 0.04146 / 2.87 ( 634) hydrogen bonds : angle 3.13991 / 2.30 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.58 seconds wall clock time: 44 minutes 24.84 seconds (2664.84 seconds total)