Starting phenix.real_space_refine on Fri Oct 23 08:47:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sdt_54792/10_2026/9sdt_54792.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sdt_54792/10_2026/9sdt_54792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sdt_54792/10_2026/9sdt_54792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sdt_54792/10_2026/9sdt_54792.map" model { file = "/net/cci-nas-00/data/ceres_data/9sdt_54792/10_2026/9sdt_54792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sdt_54792/10_2026/9sdt_54792.cif" } resolution = 2.3 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 6349 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 7 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: 9212 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: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "B" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "D" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "G" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 128 Unusual residues: {'C14': 3, 'D10': 2, 'D12': 1, 'OCT': 2, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 2.06, per 1000 atoms: 0.22 Number of scatterers: 9212 At special positions: 0 Unit cell: (87.978, 87.032, 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 6349 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: 1.01 Conformation dependent library (CDL) restraints added in 319.1 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, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 8 through 41 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 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'B' and resid 8 through 41 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 Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'C' and resid 8 through 41 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 Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'D' and resid 8 through 41 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 Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'E' and resid 8 through 41 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 Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'F' and resid 8 through 41 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 Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'G' and resid 8 through 41 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 Processing helix chain 'G' and resid 149 through 154 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 126 removed outlier: 3.614A pdb=" N ILE B 145 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 129 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.622A pdb=" N SER A 129 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 145 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 126 removed outlier: 3.615A pdb=" N ILE C 145 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 129 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 123 through 126 removed outlier: 3.615A pdb=" N ILE D 145 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 129 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 123 through 126 removed outlier: 3.615A pdb=" N ILE E 145 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 129 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 123 through 126 removed outlier: 3.615A pdb=" N ILE F 145 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER F 129 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 123 through 126 removed outlier: 3.614A pdb=" N ILE G 145 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER G 129 " --> pdb=" O LYS G 136 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1974 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: 1.26 Time building geometry restraints manager: 1.28 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: 1327 1.32 - 1.44: 2130 1.44 - 1.56: 5783 1.56 - 1.69: 14 1.69 - 1.81: 35 Bond restraints: 9289 Sorted by residual: bond pdb=" C38 PEE F 206 " pdb=" C39 PEE F 206 " ideal model delta sigma weight residual 1.523 1.318 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C38 PEE D 205 " pdb=" C39 PEE D 205 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C38 PEE A 205 " pdb=" C39 PEE A 205 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C38 PEE E 205 " pdb=" C39 PEE E 205 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C38 PEE G 201 " pdb=" C39 PEE G 201 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 9284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 12173 2.91 - 5.82: 84 5.82 - 8.73: 21 8.73 - 11.65: 0 11.65 - 14.56: 14 Bond angle restraints: 12292 Sorted by residual: angle pdb=" C38 PEE A 205 " pdb=" C39 PEE A 205 " pdb=" C40 PEE A 205 " ideal model delta sigma weight residual 112.47 127.03 -14.56 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C38 PEE D 205 " pdb=" C39 PEE D 205 " pdb=" C40 PEE D 205 " ideal model delta sigma weight residual 112.47 126.97 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C38 PEE F 206 " pdb=" C39 PEE F 206 " pdb=" C40 PEE F 206 " ideal model delta sigma weight residual 112.47 126.96 -14.49 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C38 PEE G 201 " pdb=" C39 PEE G 201 " pdb=" C40 PEE G 201 " ideal model delta sigma weight residual 112.47 126.96 -14.49 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C38 PEE B 205 " pdb=" C39 PEE B 205 " pdb=" C40 PEE B 205 " ideal model delta sigma weight residual 112.47 126.95 -14.48 3.00e+00 1.11e-01 2.33e+01 ... (remaining 12287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.64: 5509 31.64 - 63.27: 105 63.27 - 94.91: 7 94.91 - 126.55: 7 126.55 - 158.19: 7 Dihedral angle restraints: 5635 sinusoidal: 2499 harmonic: 3136 Sorted by residual: dihedral pdb=" C4 PEE E 205 " pdb=" O4P PEE E 205 " pdb=" P PEE E 205 " pdb=" O3P PEE E 205 " ideal model delta sinusoidal sigma weight residual 171.78 13.59 158.19 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C4 PEE F 206 " pdb=" O4P PEE F 206 " pdb=" P PEE F 206 " pdb=" O3P PEE F 206 " ideal model delta sinusoidal sigma weight residual 171.78 13.61 158.17 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C4 PEE C 205 " pdb=" O4P PEE C 205 " pdb=" P PEE C 205 " pdb=" O3P PEE C 205 " ideal model delta sinusoidal sigma weight residual 171.78 13.62 158.16 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 5632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1105 0.041 - 0.082: 244 0.082 - 0.123: 106 0.123 - 0.164: 1 0.164 - 0.205: 14 Chirality restraints: 1470 Sorted by residual: chirality pdb=" C2 PEE D 205 " pdb=" C1 PEE D 205 " pdb=" C3 PEE D 205 " pdb=" O2 PEE D 205 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2 PEE A 205 " pdb=" C1 PEE A 205 " pdb=" C3 PEE A 205 " pdb=" O2 PEE A 205 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C2 PEE E 205 " pdb=" C1 PEE E 205 " pdb=" C3 PEE E 205 " pdb=" O2 PEE E 205 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1467 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D 91 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C MET D 91 " 0.025 2.00e-02 2.50e+03 pdb=" O MET D 91 " -0.010 2.00e-02 2.50e+03 pdb=" N SER D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 91 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C MET B 91 " 0.025 2.00e-02 2.50e+03 pdb=" O MET B 91 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 91 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C MET A 91 " 0.025 2.00e-02 2.50e+03 pdb=" O MET A 91 " -0.009 2.00e-02 2.50e+03 pdb=" N SER A 92 " -0.008 2.00e-02 2.50e+03 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2926 2.85 - 3.36: 8748 3.36 - 3.87: 14690 3.87 - 4.39: 17228 4.39 - 4.90: 29858 Nonbonded interactions: 73450 Sorted by model distance: nonbonded pdb=" NH1 ARG A 159 " pdb=" OE1 GLU B 144 " model vdw 2.337 3.120 nonbonded pdb=" NH1 ARG F 159 " pdb=" OE1 GLU G 144 " model vdw 2.355 3.120 nonbonded pdb=" OD1 ASN B 150 " pdb=" N LEU B 151 " model vdw 2.393 3.120 nonbonded pdb=" OD1 ASN E 150 " pdb=" N LEU E 151 " model vdw 2.394 3.120 nonbonded pdb=" OD1 ASN C 150 " pdb=" N LEU C 151 " model vdw 2.394 3.120 ... (remaining 73445 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: 0.03 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: 0.560 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.010 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: 0.020 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 0.205 9289 Z= 0.390 Angle : 0.768 14.558 12292 Z= 0.353 Chirality : 0.046 0.205 1470 Planarity : 0.003 0.020 1379 Dihedral : 15.050 158.185 3633 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1085 helix: 2.99 (0.18), residues: 721 sheet: -1.10 (0.51), residues: 105 loop : -0.40 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 159 TYR 0.016 0.001 TYR C 56 PHE 0.007 0.001 PHE G 87 TRP 0.002 0.000 TRP G 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.39 ( 9289) covalent geometry : angle 0.76791 / 0.35 (12292) hydrogen bonds : bond 0.11184 / 7.65 ( 679) hydrogen bonds : angle 4.39242 / 3.19 ( 1974) *********************** 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 132 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.324 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.5442 time to fit residues: 76.7199 Evaluate side-chains 103 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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: 0.6980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.165963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135323 restraints weight = 9175.388| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.61 r_work: 0.3532 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9289 Z= 0.123 Angle : 0.598 13.521 12292 Z= 0.280 Chirality : 0.041 0.127 1470 Planarity : 0.003 0.028 1379 Dihedral : 14.881 141.149 1834 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.32 % Allowed : 6.08 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.82 (0.26), residues: 1085 helix: 3.13 (0.18), residues: 721 sheet: -0.88 (0.57), residues: 105 loop : -0.73 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.018 0.001 TYR E 56 PHE 0.011 0.002 PHE G 87 TRP 0.001 0.000 TRP C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 9289) covalent geometry : angle 0.59835 / 0.28 (12292) hydrogen bonds : bond 0.04893 / 3.38 ( 679) hydrogen bonds : angle 3.65090 / 2.69 ( 1974) *********************** 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: 3 poor density : 122 time to evaluate : 0.333 Fit side-chains REVERT: B 119 ASP cc_start: 0.8614 (t70) cc_final: 0.8360 (t70) REVERT: D 30 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8254 (mttm) REVERT: D 91 MET cc_start: 0.5678 (tmm) cc_final: 0.5422 (tmm) REVERT: D 144 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8263 (tt0) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.5397 time to fit residues: 72.3227 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 144 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [20, 78, 52, 46, 82, 54, 84, 53, 37, 26, 51] chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.153524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119962 restraints weight = 8976.971| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.75 r_work: 0.3222 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9289 Z= 0.136 Angle : 0.563 14.655 12292 Z= 0.274 Chirality : 0.041 0.130 1470 Planarity : 0.003 0.032 1379 Dihedral : 15.111 142.261 1834 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % 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: 2.76 (0.25), residues: 1085 helix: 3.04 (0.17), residues: 728 sheet: -0.50 (0.55), residues: 105 loop : -0.93 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 159 TYR 0.016 0.001 TYR C 56 PHE 0.009 0.001 PHE C 120 TRP 0.001 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 9289) covalent geometry : angle 0.56292 / 0.27 (12292) hydrogen bonds : bond 0.05150 / 3.55 ( 679) hydrogen bonds : angle 3.63538 / 2.68 ( 1974) *********************** 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 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.336 Fit side-chains REVERT: B 119 ASP cc_start: 0.8340 (t70) cc_final: 0.8056 (t70) REVERT: D 91 MET cc_start: 0.5886 (tmm) cc_final: 0.5538 (tmm) outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 0.4970 time to fit residues: 66.4837 Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [13, 84, 38, 11, 24, 33, 31, 93, 41, 75, 81] chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.151033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117123 restraints weight = 9056.946| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.76 r_work: 0.3183 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9289 Z= 0.165 Angle : 0.580 11.839 12292 Z= 0.291 Chirality : 0.042 0.126 1470 Planarity : 0.003 0.031 1379 Dihedral : 15.405 141.527 1834 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.28 % Allowed : 8.10 % Favored : 90.62 % 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: 2.58 (0.24), residues: 1085 helix: 2.87 (0.17), residues: 728 sheet: -0.41 (0.51), residues: 105 loop : -0.96 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 159 TYR 0.014 0.001 TYR D 56 PHE 0.010 0.002 PHE A 160 TRP 0.002 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 9289) covalent geometry : angle 0.58026 / 0.29 (12292) hydrogen bonds : bond 0.05595 / 3.86 ( 679) hydrogen bonds : angle 3.72551 / 2.74 ( 1974) *********************** 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 141 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.321 Fit side-chains REVERT: B 119 ASP cc_start: 0.8315 (t70) cc_final: 0.8061 (t70) REVERT: B 124 LYS cc_start: 0.8510 (mptt) cc_final: 0.7823 (mtpm) REVERT: C 30 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7599 (mptm) REVERT: C 91 MET cc_start: 0.5922 (tmm) cc_final: 0.5432 (tmm) REVERT: D 91 MET cc_start: 0.5945 (tmm) cc_final: 0.5421 (tmm) REVERT: D 124 LYS cc_start: 0.8543 (mptt) cc_final: 0.7885 (mtpm) REVERT: F 113 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: F 124 LYS cc_start: 0.8554 (mptt) cc_final: 0.8011 (mtpm) REVERT: F 136 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.7129 (mptt) outliers start: 12 outliers final: 3 residues processed: 134 average time/residue: 0.5026 time to fit residues: 72.4374 Evaluate side-chains 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 136 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [60, 87, 103, 33, 15, 56, 45, 70, 65, 68, 93] chunk 60 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 33 optimal weight: 0.0270 chunk 15 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.153740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120371 restraints weight = 9056.383| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.75 r_work: 0.3228 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9289 Z= 0.116 Angle : 0.515 13.054 12292 Z= 0.253 Chirality : 0.041 0.138 1470 Planarity : 0.003 0.030 1379 Dihedral : 14.692 142.639 1834 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.85 % Allowed : 10.34 % Favored : 88.81 % 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: 2.78 (0.24), residues: 1085 helix: 3.05 (0.17), residues: 721 sheet: -0.51 (0.53), residues: 105 loop : -0.75 (0.31), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 159 TYR 0.014 0.001 TYR D 56 PHE 0.009 0.001 PHE A 87 TRP 0.001 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 ( 9289) covalent geometry : angle 0.51462 / 0.25 (12292) hydrogen bonds : bond 0.04700 / 3.24 ( 679) hydrogen bonds : angle 3.58409 / 2.63 ( 1974) *********************** 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 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.339 Fit side-chains REVERT: B 119 ASP cc_start: 0.8172 (t70) cc_final: 0.7930 (t70) REVERT: B 124 LYS cc_start: 0.8455 (mptt) cc_final: 0.7740 (mtpm) REVERT: C 30 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7424 (mptm) REVERT: C 91 MET cc_start: 0.5790 (tmm) cc_final: 0.5360 (tmm) REVERT: D 91 MET cc_start: 0.5988 (tmm) cc_final: 0.5725 (tmm) REVERT: F 124 LYS cc_start: 0.8486 (mptt) cc_final: 0.7891 (mtpm) outliers start: 8 outliers final: 3 residues processed: 134 average time/residue: 0.4842 time to fit residues: 69.9494 Evaluate side-chains 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain G residue 12 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [33, 60, 25, 35, 75, 49, 55, 29, 14, 92, 34] chunk 33 optimal weight: 0.0270 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.156240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123585 restraints weight = 9069.682| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.70 r_work: 0.3267 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9289 Z= 0.107 Angle : 0.486 9.566 12292 Z= 0.241 Chirality : 0.041 0.133 1470 Planarity : 0.003 0.028 1379 Dihedral : 14.337 144.358 1834 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.07 % Allowed : 11.30 % Favored : 87.63 % 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: 2.82 (0.24), residues: 1085 helix: 3.10 (0.17), residues: 714 sheet: -0.51 (0.52), residues: 105 loop : -0.69 (0.30), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 159 TYR 0.015 0.001 TYR D 56 PHE 0.011 0.001 PHE G 87 TRP 0.001 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 ( 9289) covalent geometry : angle 0.48624 / 0.24 (12292) hydrogen bonds : bond 0.04414 / 3.03 ( 679) hydrogen bonds : angle 3.57045 / 2.61 ( 1974) *********************** 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 143 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.264 Fit side-chains REVERT: B 124 LYS cc_start: 0.8631 (mptt) cc_final: 0.8110 (mtpm) REVERT: C 30 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7882 (mptm) REVERT: C 124 LYS cc_start: 0.8638 (mptt) cc_final: 0.8121 (mtpt) REVERT: D 91 MET cc_start: 0.5869 (tmm) cc_final: 0.5293 (tmm) REVERT: D 124 LYS cc_start: 0.8627 (mptt) cc_final: 0.8094 (mmmt) REVERT: F 113 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: F 124 LYS cc_start: 0.8655 (mptt) cc_final: 0.8176 (mtpm) REVERT: G 124 LYS cc_start: 0.8619 (mptt) cc_final: 0.8117 (mtpm) outliers start: 10 outliers final: 3 residues processed: 137 average time/residue: 0.4847 time to fit residues: 71.4330 Evaluate side-chains 132 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain F residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [93, 21, 57, 25, 84, 62, 24, 96, 91, 45, 87] chunk 93 optimal weight: 0.0170 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.157389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124889 restraints weight = 9064.523| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.69 r_work: 0.3283 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9289 Z= 0.101 Angle : 0.474 9.168 12292 Z= 0.235 Chirality : 0.040 0.133 1470 Planarity : 0.003 0.026 1379 Dihedral : 14.141 146.154 1834 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.07 % Allowed : 11.94 % Favored : 86.99 % 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: 2.84 (0.24), residues: 1085 helix: 3.09 (0.17), residues: 714 sheet: -0.58 (0.51), residues: 105 loop : -0.56 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 159 TYR 0.014 0.001 TYR D 56 PHE 0.012 0.001 PHE G 87 TRP 0.001 0.000 TRP D 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 ( 9289) covalent geometry : angle 0.47399 / 0.23 (12292) hydrogen bonds : bond 0.04216 / 2.89 ( 679) hydrogen bonds : angle 3.56242 / 2.60 ( 1974) *********************** 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 145 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.328 Fit side-chains REVERT: B 30 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8136 (mmtm) REVERT: B 119 ASP cc_start: 0.8697 (t70) cc_final: 0.8455 (t70) REVERT: B 124 LYS cc_start: 0.8603 (mptt) cc_final: 0.8043 (mtpm) REVERT: C 30 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7912 (mptm) REVERT: C 124 LYS cc_start: 0.8649 (mptt) cc_final: 0.8122 (mtpt) REVERT: D 124 LYS cc_start: 0.8595 (mptt) cc_final: 0.8102 (mmmt) REVERT: F 124 LYS cc_start: 0.8642 (mptt) cc_final: 0.8171 (mtpm) REVERT: G 124 LYS cc_start: 0.8628 (mptt) cc_final: 0.8104 (mtpm) outliers start: 10 outliers final: 1 residues processed: 137 average time/residue: 0.4856 time to fit residues: 71.6512 Evaluate side-chains 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain D residue 30 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [49, 36, 102, 34, 0, 64, 59, 13, 29, 40, 80] chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.155700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122988 restraints weight = 8978.623| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.69 r_work: 0.3260 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9289 Z= 0.114 Angle : 0.502 8.363 12292 Z= 0.247 Chirality : 0.041 0.125 1470 Planarity : 0.003 0.027 1379 Dihedral : 14.292 147.305 1834 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.85 % Allowed : 12.26 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.76 (0.24), residues: 1085 helix: 2.98 (0.17), residues: 714 sheet: -0.57 (0.51), residues: 105 loop : -0.46 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.015 0.001 TYR D 56 PHE 0.010 0.001 PHE G 87 TRP 0.001 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 9289) covalent geometry : angle 0.50191 / 0.25 (12292) hydrogen bonds : bond 0.04519 / 3.11 ( 679) hydrogen bonds : angle 3.60733 / 2.63 ( 1974) *********************** 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 145 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.207 Fit side-chains REVERT: A 124 LYS cc_start: 0.8615 (mptt) cc_final: 0.8125 (mmpt) REVERT: B 30 LYS cc_start: 0.8388 (mmtp) cc_final: 0.8149 (mmtm) REVERT: B 119 ASP cc_start: 0.8648 (t70) cc_final: 0.8412 (t70) REVERT: B 124 LYS cc_start: 0.8669 (mptt) cc_final: 0.8145 (mtpm) REVERT: C 124 LYS cc_start: 0.8685 (mptt) cc_final: 0.8167 (mtpp) REVERT: D 124 LYS cc_start: 0.8620 (mptt) cc_final: 0.8125 (mmmt) REVERT: F 91 MET cc_start: 0.5320 (ppp) cc_final: 0.5005 (tmm) REVERT: F 124 LYS cc_start: 0.8634 (mptt) cc_final: 0.8153 (mtpp) REVERT: G 124 LYS cc_start: 0.8645 (mptt) cc_final: 0.8133 (mtpm) outliers start: 8 outliers final: 4 residues processed: 140 average time/residue: 0.5045 time to fit residues: 75.8710 Evaluate side-chains 130 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain E residue 91 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [56, 92, 103, 97, 98, 26, 21, 54, 27, 13, 60] chunk 56 optimal weight: 0.0040 chunk 92 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 97 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 overall best weight: 0.1768 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.166204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135523 restraints weight = 9250.324| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.63 r_work: 0.3497 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9289 Z= 0.088 Angle : 0.449 8.397 12292 Z= 0.221 Chirality : 0.040 0.126 1470 Planarity : 0.002 0.022 1379 Dihedral : 13.811 148.552 1834 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.43 % Allowed : 13.22 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.90 (0.24), residues: 1085 helix: 3.06 (0.18), residues: 714 sheet: -0.69 (0.52), residues: 105 loop : -0.22 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 159 TYR 0.014 0.001 TYR D 56 PHE 0.013 0.001 PHE E 87 TRP 0.003 0.000 TRP C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.09 ( 9289) covalent geometry : angle 0.44910 / 0.22 (12292) hydrogen bonds : bond 0.03704 / 2.53 ( 679) hydrogen bonds : angle 3.58475 / 2.59 ( 1974) *********************** 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 143 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.297 Fit side-chains REVERT: B 119 ASP cc_start: 0.8608 (t70) cc_final: 0.8369 (t70) REVERT: B 124 LYS cc_start: 0.8652 (mptt) cc_final: 0.8246 (mtpm) REVERT: C 124 LYS cc_start: 0.8623 (mptt) cc_final: 0.8232 (mtpt) REVERT: D 124 LYS cc_start: 0.8533 (mptt) cc_final: 0.8190 (mmmt) REVERT: F 91 MET cc_start: 0.4931 (ppp) cc_final: 0.4725 (tmm) REVERT: F 124 LYS cc_start: 0.8661 (mptt) cc_final: 0.8241 (mtpp) REVERT: G 124 LYS cc_start: 0.8616 (mptt) cc_final: 0.8215 (mtpm) outliers start: 4 outliers final: 2 residues processed: 141 average time/residue: 0.5037 time to fit residues: 76.2479 Evaluate side-chains 132 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain D residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [1, 25, 0, 36, 104, 98, 86, 65, 80, 33, 82] chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.152800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119430 restraints weight = 9064.044| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.71 r_work: 0.3213 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9289 Z= 0.171 Angle : 0.581 8.590 12292 Z= 0.288 Chirality : 0.043 0.145 1470 Planarity : 0.003 0.026 1379 Dihedral : 14.823 150.411 1834 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.85 % Allowed : 13.22 % 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: 2.36 (0.24), residues: 1085 helix: 2.63 (0.17), residues: 728 sheet: -0.57 (0.50), residues: 105 loop : -0.73 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.019 0.001 TYR C 56 PHE 0.009 0.002 PHE E 59 TRP 0.002 0.001 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 9289) covalent geometry : angle 0.58064 / 0.29 (12292) hydrogen bonds : bond 0.05347 / 3.67 ( 679) hydrogen bonds : angle 3.74999 / 2.74 ( 1974) ********************** 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 131 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.250 Fit side-chains REVERT: A 124 LYS cc_start: 0.8662 (mptt) cc_final: 0.8162 (mtpm) REVERT: B 119 ASP cc_start: 0.8689 (t70) cc_final: 0.8418 (t70) REVERT: B 124 LYS cc_start: 0.8667 (mptt) cc_final: 0.8135 (mtpm) REVERT: C 124 LYS cc_start: 0.8722 (mptt) cc_final: 0.8172 (mtpp) REVERT: D 124 LYS cc_start: 0.8671 (mptt) cc_final: 0.8161 (mmmt) REVERT: F 91 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.5097 (tmm) REVERT: F 124 LYS cc_start: 0.8687 (mptt) cc_final: 0.8248 (mtpm) REVERT: G 124 LYS cc_start: 0.8712 (mptt) cc_final: 0.8193 (mtpm) outliers start: 8 outliers final: 4 residues processed: 125 average time/residue: 0.4953 time to fit residues: 66.7035 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain G residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [6, 99, 57, 27, 97, 1, 88, 46, 98, 81, 87] chunk 6 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 57 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 0.0030 overall best weight: 0.7604 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.154972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122255 restraints weight = 8874.300| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.67 r_work: 0.3248 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9289 Z= 0.120 Angle : 0.518 8.680 12292 Z= 0.256 Chirality : 0.041 0.126 1470 Planarity : 0.003 0.026 1379 Dihedral : 14.540 151.462 1834 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.75 % Allowed : 13.43 % Favored : 85.82 % 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: 2.58 (0.24), residues: 1085 helix: 2.75 (0.17), residues: 714 sheet: -0.61 (0.50), residues: 105 loop : -0.22 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 159 TYR 0.015 0.001 TYR C 56 PHE 0.011 0.001 PHE E 87 TRP 0.001 0.000 TRP F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 9289) covalent geometry : angle 0.51812 / 0.26 (12292) hydrogen bonds : bond 0.04657 / 3.20 ( 679) hydrogen bonds : angle 3.67570 / 2.68 ( 1974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.60 seconds wall clock time: 58 minutes 39.55 seconds (3519.55 seconds total)