Starting phenix.real_space_refine on Mon Nov 18 00:44:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/11_2024/8ouz_17206_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/11_2024/8ouz_17206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/11_2024/8ouz_17206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/11_2024/8ouz_17206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/11_2024/8ouz_17206_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/11_2024/8ouz_17206_trim.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 49 5.16 5 C 4603 2.51 5 N 1267 2.21 5 O 1519 1.98 5 H 7373 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1132 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "B" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4960 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 2 Chain: "C" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4722 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 7, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3774 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 7.72, per 1000 atoms: 0.52 Number of scatterers: 14822 At special positions: 0 Unit cell: (93.7125, 103.275, 93.7125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 8 15.00 Mg 3 11.99 O 1519 8.00 N 1267 7.00 C 4603 6.00 H 7373 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 6 sheets defined 52.6% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.639A pdb=" N VAL A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 10' Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 26 through 32 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.664A pdb=" N ALA A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.826A pdb=" N LEU B 39 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 87 through 97 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 143 through 144 No H-bonds generated for 'chain 'B' and resid 143 through 144' Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 165 through 185 removed outlier: 3.807A pdb=" N VAL B 169 " --> pdb=" O MET B 165 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.141A pdb=" N LYS B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 215 through 232 Proline residue: B 227 - end of helix removed outlier: 3.811A pdb=" N GLU B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 266 through 276 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 33 Processing helix chain 'C' and resid 35 through 42 Processing helix chain 'C' and resid 46 through 62 Processing helix chain 'C' and resid 68 through 79 removed outlier: 3.715A pdb=" N THR C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 Processing helix chain 'C' and resid 112 through 127 Processing helix chain 'C' and resid 142 through 152 Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 174 through 192 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.816A pdb=" N VAL C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'C' and resid 221 through 240 Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.804A pdb=" N PHE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 53 through 67 Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 88 through 100 Processing helix chain 'D' and resid 104 through 113 Processing helix chain 'D' and resid 122 through 140 removed outlier: 3.985A pdb=" N GLU D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.768A pdb=" N GLY D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 170 through 187 Processing helix chain 'D' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 5.636A pdb=" N GLU B 154 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR B 121 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASN B 284 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 123 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG B 312 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.916A pdb=" N CYS B 85 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 132 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL C 170 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR C 134 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 203 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N THR C 248 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 205 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG C 275 " --> pdb=" O ALA C 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 340 through 342 Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.972A pdb=" N GLU D 77 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE D 147 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU D 79 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP D 149 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE D 81 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS D 144 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE D 192 " --> pdb=" O CYS D 144 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU D 146 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR D 194 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU D 148 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N GLN D 196 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP D 42 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA D 193 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 44 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR D 195 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE D 46 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS D 237 " --> pdb=" O ILE D 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AA6, first strand: chain 'C' and resid 251 through 253 374 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7345 1.03 - 1.23: 31 1.23 - 1.42: 2984 1.42 - 1.62: 4363 1.62 - 1.81: 70 Bond restraints: 14793 Sorted by residual: bond pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.43e+00 bond pdb=" N GLY C 2 " pdb=" CA GLY C 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.96e+00 bond pdb=" N GLN B 11 " pdb=" CA GLN B 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N LYS A 4 " pdb=" CA LYS A 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N GLY D 20 " pdb=" H GLY D 20 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 14788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 26191 1.43 - 2.86: 493 2.86 - 4.30: 46 4.30 - 5.73: 16 5.73 - 7.16: 8 Bond angle restraints: 26754 Sorted by residual: angle pdb=" C3' ATP D 301 " pdb=" C2' ATP D 301 " pdb=" O2' ATP D 301 " ideal model delta sigma weight residual 111.83 104.67 7.16 2.67e+00 1.40e-01 7.20e+00 angle pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" C5' ATP C 401 " ideal model delta sigma weight residual 115.19 110.70 4.49 1.76e+00 3.23e-01 6.50e+00 angle pdb=" C3' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" C5' ATP D 301 " ideal model delta sigma weight residual 115.19 110.75 4.44 1.76e+00 3.23e-01 6.37e+00 angle pdb=" C2' ATP D 301 " pdb=" C3' ATP D 301 " pdb=" O3' ATP D 301 " ideal model delta sigma weight residual 111.83 105.24 6.59 2.67e+00 1.40e-01 6.10e+00 angle pdb=" C3' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" O4' ATP D 301 " ideal model delta sigma weight residual 105.22 102.02 3.20 1.30e+00 5.94e-01 6.09e+00 ... (remaining 26749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.10: 6562 29.10 - 58.20: 311 58.20 - 87.29: 34 87.29 - 116.39: 3 116.39 - 145.49: 1 Dihedral angle restraints: 6911 sinusoidal: 3876 harmonic: 3035 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.49 -145.49 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -171.86 111.86 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 36.74 -96.74 1 2.00e+01 2.50e-03 2.68e+01 ... (remaining 6908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1042 0.060 - 0.119: 111 0.119 - 0.179: 17 0.179 - 0.239: 0 0.239 - 0.298: 6 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C2' ATP D 301 " pdb=" C1' ATP D 301 " pdb=" C3' ATP D 301 " pdb=" O2' ATP D 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ATP D 301 " pdb=" C2' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" O3' ATP D 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1173 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 34 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A 35 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 307 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" CD GLU C 307 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU C 307 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU C 307 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 263 " -0.005 2.00e-02 2.50e+03 9.70e-03 9.41e-01 pdb=" C ASN B 263 " 0.017 2.00e-02 2.50e+03 pdb=" O ASN B 263 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY B 264 " -0.006 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 385 2.13 - 2.75: 27064 2.75 - 3.37: 42365 3.37 - 3.98: 55218 3.98 - 4.60: 86854 Nonbonded interactions: 211886 Sorted by model distance: nonbonded pdb=" HG1 THR B 132 " pdb="MG MG B 402 " model vdw 1.513 1.700 nonbonded pdb=" OE1 GLN D 200 " pdb=" H GLN D 200 " model vdw 1.534 2.450 nonbonded pdb=" HG1 THR D 55 " pdb="MG MG D 302 " model vdw 1.548 1.700 nonbonded pdb=" O ILE D 66 " pdb="HH21 ARG D 114 " model vdw 1.652 2.450 nonbonded pdb=" OE1 GLU C 104 " pdb="HH11 ARG C 275 " model vdw 1.652 2.450 ... (remaining 211881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.630 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: 0.300 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 34.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.003 0.041 7420 Z= 0.180 Angle : 0.561 7.161 10033 Z= 0.290 Chirality : 0.044 0.298 1176 Planarity : 0.003 0.031 1256 Dihedral : 16.592 145.487 2805 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.00 % Allowed : 12.84 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.28), residues: 906 helix: 1.66 (0.26), residues: 423 sheet: 0.45 (0.41), residues: 163 loop : -0.43 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.004 0.001 HIS B 179 PHE 0.010 0.001 PHE C 176 TYR 0.009 0.001 TYR D 119 ARG 0.006 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 100 average time/residue: 3.0991 time to fit residues: 326.3184 Evaluate side-chains 88 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7420 Z= 0.233 Angle : 0.558 7.397 10033 Z= 0.293 Chirality : 0.040 0.141 1176 Planarity : 0.004 0.044 1256 Dihedral : 10.303 126.533 1077 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.24 % Allowed : 12.59 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.28), residues: 906 helix: 1.32 (0.25), residues: 438 sheet: 0.31 (0.41), residues: 164 loop : -0.33 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 268 HIS 0.006 0.001 HIS D 60 PHE 0.011 0.001 PHE D 115 TYR 0.011 0.002 TYR D 155 ARG 0.007 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 224 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.5974 (ttt180) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 2.7479 time to fit residues: 299.6597 Evaluate side-chains 98 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 224 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7420 Z= 0.207 Angle : 0.534 6.989 10033 Z= 0.278 Chirality : 0.039 0.138 1176 Planarity : 0.004 0.035 1256 Dihedral : 9.955 107.868 1074 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.37 % Allowed : 12.47 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 906 helix: 1.32 (0.25), residues: 438 sheet: 0.25 (0.40), residues: 163 loop : -0.38 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 268 HIS 0.003 0.001 HIS B 276 PHE 0.011 0.001 PHE D 115 TYR 0.010 0.001 TYR D 155 ARG 0.005 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 ILE cc_start: 0.7798 (mt) cc_final: 0.7583 (mt) REVERT: D 224 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.5928 (ttt180) REVERT: D 229 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7905 (tmtm) REVERT: D 239 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7869 (mtt) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 2.5884 time to fit residues: 304.6939 Evaluate side-chains 103 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7420 Z= 0.208 Angle : 0.536 6.809 10033 Z= 0.278 Chirality : 0.039 0.137 1176 Planarity : 0.003 0.035 1256 Dihedral : 9.595 103.583 1074 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.37 % Allowed : 13.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 906 helix: 1.34 (0.25), residues: 438 sheet: 0.18 (0.39), residues: 165 loop : -0.38 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 268 HIS 0.003 0.001 HIS D 60 PHE 0.011 0.001 PHE D 115 TYR 0.009 0.001 TYR D 155 ARG 0.005 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 ILE cc_start: 0.7806 (mt) cc_final: 0.7595 (mt) REVERT: D 224 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.5921 (ttt180) REVERT: D 229 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7911 (tmtm) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 2.6613 time to fit residues: 293.1721 Evaluate side-chains 100 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 224 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7420 Z= 0.265 Angle : 0.578 6.367 10033 Z= 0.302 Chirality : 0.041 0.141 1176 Planarity : 0.004 0.037 1256 Dihedral : 9.463 106.171 1073 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.37 % Allowed : 13.59 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 906 helix: 1.12 (0.25), residues: 437 sheet: 0.16 (0.40), residues: 165 loop : -0.50 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 268 HIS 0.004 0.001 HIS D 60 PHE 0.014 0.002 PHE D 80 TYR 0.012 0.002 TYR D 155 ARG 0.005 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 ILE cc_start: 0.7856 (mt) cc_final: 0.7644 (mt) REVERT: C 184 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 224 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.5870 (ttt180) REVERT: D 229 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7905 (tmtm) REVERT: D 239 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7929 (mtt) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 2.6875 time to fit residues: 310.3069 Evaluate side-chains 106 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7420 Z= 0.237 Angle : 0.560 6.696 10033 Z= 0.292 Chirality : 0.040 0.147 1176 Planarity : 0.004 0.038 1256 Dihedral : 9.452 110.875 1073 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 14.09 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 906 helix: 1.16 (0.25), residues: 437 sheet: 0.09 (0.39), residues: 173 loop : -0.52 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 314 HIS 0.003 0.001 HIS D 237 PHE 0.012 0.001 PHE D 115 TYR 0.011 0.002 TYR D 155 ARG 0.004 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 ILE cc_start: 0.7851 (mt) cc_final: 0.7650 (mt) REVERT: D 224 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.5859 (ttt180) REVERT: D 229 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7905 (tmtm) REVERT: D 239 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7882 (mtt) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 2.7318 time to fit residues: 300.4832 Evaluate side-chains 103 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7420 Z= 0.196 Angle : 0.537 6.490 10033 Z= 0.278 Chirality : 0.039 0.148 1176 Planarity : 0.003 0.037 1256 Dihedral : 8.997 105.473 1071 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.12 % Allowed : 14.84 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 906 helix: 1.29 (0.25), residues: 438 sheet: 0.09 (0.39), residues: 173 loop : -0.49 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 268 HIS 0.004 0.001 HIS D 86 PHE 0.011 0.001 PHE D 115 TYR 0.009 0.001 TYR D 155 ARG 0.004 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 ILE cc_start: 0.7842 (mt) cc_final: 0.7630 (mt) REVERT: C 184 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7793 (mt-10) REVERT: D 224 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.5881 (ttt180) REVERT: D 229 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7903 (tmtm) REVERT: D 239 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7801 (mtt) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 2.6751 time to fit residues: 295.5246 Evaluate side-chains 106 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 23 HIS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7420 Z= 0.203 Angle : 0.543 6.484 10033 Z= 0.281 Chirality : 0.039 0.150 1176 Planarity : 0.003 0.036 1256 Dihedral : 8.981 104.839 1071 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.24 % Allowed : 15.21 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.28), residues: 906 helix: 1.27 (0.25), residues: 438 sheet: 0.07 (0.39), residues: 172 loop : -0.48 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 268 HIS 0.003 0.001 HIS B 179 PHE 0.011 0.001 PHE D 115 TYR 0.009 0.001 TYR D 155 ARG 0.004 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 ILE cc_start: 0.7846 (mt) cc_final: 0.7636 (mt) REVERT: D 224 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.5884 (ttt180) REVERT: D 229 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7902 (tmtm) REVERT: D 239 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7849 (mtt) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 2.6759 time to fit residues: 289.0809 Evaluate side-chains 103 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 23 HIS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7420 Z= 0.194 Angle : 0.538 6.487 10033 Z= 0.278 Chirality : 0.039 0.146 1176 Planarity : 0.003 0.036 1256 Dihedral : 8.896 102.647 1071 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.24 % Allowed : 15.21 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.28), residues: 906 helix: 1.32 (0.25), residues: 438 sheet: 0.08 (0.39), residues: 172 loop : -0.50 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 268 HIS 0.004 0.001 HIS B 179 PHE 0.011 0.001 PHE D 115 TYR 0.009 0.001 TYR D 155 ARG 0.004 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 ILE cc_start: 0.7844 (mt) cc_final: 0.7635 (mt) REVERT: D 224 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.5886 (ttt180) REVERT: D 229 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7902 (tmtm) REVERT: D 239 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7846 (mtt) outliers start: 18 outliers final: 13 residues processed: 101 average time/residue: 2.6371 time to fit residues: 282.0672 Evaluate side-chains 102 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 23 HIS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7420 Z= 0.202 Angle : 0.544 6.500 10033 Z= 0.282 Chirality : 0.039 0.144 1176 Planarity : 0.003 0.036 1256 Dihedral : 8.903 102.366 1071 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.12 % Allowed : 15.46 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 906 helix: 1.30 (0.25), residues: 438 sheet: 0.08 (0.39), residues: 172 loop : -0.49 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 268 HIS 0.004 0.001 HIS B 179 PHE 0.011 0.001 PHE D 115 TYR 0.009 0.001 TYR D 155 ARG 0.004 0.000 ARG B 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 224 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.5885 (ttt180) REVERT: D 239 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7866 (mtt) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 2.7001 time to fit residues: 282.9761 Evaluate side-chains 102 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain C residue 23 HIS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 239 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116231 restraints weight = 24848.465| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.95 r_work: 0.3462 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7420 Z= 0.179 Angle : 0.530 6.415 10033 Z= 0.273 Chirality : 0.039 0.148 1176 Planarity : 0.003 0.036 1256 Dihedral : 8.758 97.843 1071 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.00 % Allowed : 15.59 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.28), residues: 906 helix: 1.37 (0.25), residues: 440 sheet: 0.13 (0.39), residues: 170 loop : -0.49 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 314 HIS 0.004 0.001 HIS B 179 PHE 0.010 0.001 PHE D 115 TYR 0.008 0.001 TYR B 210 ARG 0.005 0.000 ARG C 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6277.87 seconds wall clock time: 111 minutes 53.57 seconds (6713.57 seconds total)