Starting phenix.real_space_refine on Sat Apr 4 23:40:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p8a_71370/04_2026/9p8a_71370.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p8a_71370/04_2026/9p8a_71370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p8a_71370/04_2026/9p8a_71370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p8a_71370/04_2026/9p8a_71370.map" model { file = "/net/cci-nas-00/data/ceres_data/9p8a_71370/04_2026/9p8a_71370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p8a_71370/04_2026/9p8a_71370.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1740 atoms to isotropic. 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 3 5.49 5 S 23 5.16 5 C 2923 2.51 5 N 848 2.21 5 O 859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4656 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 1907 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 8, 'TRANS': 331} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 936 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 760 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'ASP:plan': 24, 'GLU:plan': 28, 'ARG:plan': 24, 'ASN:plan1': 10, 'GLN:plan1': 15, 'PHE:plan': 7, 'HIS:plan': 3, 'TYR:plan': 12, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 553 Chain: "B" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2357 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 12, 'GLN:plan1': 6, 'ARG:plan': 9, 'ASN:plan1': 5, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 159 Chain: "G" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 356 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 1.24, per 1000 atoms: 0.27 Number of scatterers: 4656 At special positions: 0 Unit cell: (74.76, 98.28, 78.12, 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 23 16.00 P 3 15.00 O 859 8.00 N 848 7.00 C 2923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 425.3 milliseconds 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 36.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 11 through 38 removed outlier: 4.259A pdb=" N ARG A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 68 through 97 removed outlier: 3.503A pdb=" N LYS A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.604A pdb=" N ASP A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.512A pdb=" N GLN A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 214 through 220 removed outlier: 3.592A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 261 removed outlier: 3.606A pdb=" N GLU A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.678A pdb=" N ALA A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 347 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.702A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.595A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 231 removed outlier: 6.631A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47 removed outlier: 4.254A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.719A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.240A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.696A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.878A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.784A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 246 hydrogen bonds defined for protein. 714 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: 0.70 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1283 1.33 - 1.45: 774 1.45 - 1.57: 2634 1.57 - 1.69: 5 1.69 - 1.81: 33 Bond restraints: 4729 Sorted by residual: bond pdb=" N THR G 52 " pdb=" CA THR G 52 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.20e-02 6.94e+03 6.69e+00 bond pdb=" N VAL G 54 " pdb=" CA VAL G 54 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.68e+00 bond pdb=" C2 GTP A 401 " pdb=" N3 GTP A 401 " ideal model delta sigma weight residual 1.380 1.331 0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" N ARG G 62 " pdb=" CA ARG G 62 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.54e+00 bond pdb=" N LEU G 51 " pdb=" CA LEU G 51 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.20e-02 6.94e+03 5.23e+00 ... (remaining 4724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 6419 2.56 - 5.12: 73 5.12 - 7.68: 8 7.68 - 10.24: 6 10.24 - 12.79: 7 Bond angle restraints: 6513 Sorted by residual: angle pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sigma weight residual 120.50 133.29 -12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" PB GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sigma weight residual 120.50 131.32 -10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C1' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " ideal model delta sigma weight residual 111.00 100.32 10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" C4' GTP A 401 " ideal model delta sigma weight residual 111.00 100.52 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 119.83 -10.33 3.00e+00 1.11e-01 1.19e+01 ... (remaining 6508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 2680 34.51 - 69.01: 47 69.01 - 103.52: 2 103.52 - 138.02: 5 138.02 - 172.53: 1 Dihedral angle restraints: 2735 sinusoidal: 598 harmonic: 2137 Sorted by residual: dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 88.34 172.53 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 -49.01 -133.69 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 62.96 -131.88 1 2.00e+01 2.50e-03 4.00e+01 ... (remaining 2732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 612 0.047 - 0.095: 147 0.095 - 0.142: 39 0.142 - 0.189: 1 0.189 - 0.237: 1 Chirality restraints: 800 Sorted by residual: chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CG LEU B 14 " pdb=" CB LEU B 14 " pdb=" CD1 LEU B 14 " pdb=" CD2 LEU B 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 797 not shown) Planarity restraints: 863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO B 236 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 325 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.06e+00 pdb=" C MET B 325 " -0.025 2.00e-02 2.50e+03 pdb=" O MET B 325 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA B 326 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.009 2.00e-02 2.50e+03 6.29e-03 7.92e-01 pdb=" CG TYR B 59 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.001 2.00e-02 2.50e+03 ... (remaining 860 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 667 2.75 - 3.29: 4364 3.29 - 3.83: 7713 3.83 - 4.36: 7795 4.36 - 4.90: 14399 Nonbonded interactions: 34938 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.218 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.260 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.283 3.120 nonbonded pdb=" O LYS B 57 " pdb=" OG SER B 74 " model vdw 2.344 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.349 3.120 ... (remaining 34933 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.880 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 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 : 0.004 0.049 4729 Z= 0.213 Angle : 0.811 12.794 6513 Z= 0.423 Chirality : 0.043 0.237 800 Planarity : 0.002 0.036 863 Dihedral : 16.464 172.529 1343 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.74 % Allowed : 28.68 % Favored : 70.59 % 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: 0.24 (0.32), residues: 729 helix: 2.81 (0.33), residues: 257 sheet: -1.13 (0.38), residues: 176 loop : -1.45 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.015 0.001 TYR B 59 PHE 0.013 0.001 PHE B 241 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4729) covalent geometry : angle 0.81090 ( 6513) hydrogen bonds : bond 0.13347 ( 246) hydrogen bonds : angle 4.81120 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 316 LEU cc_start: 0.6372 (mt) cc_final: 0.5282 (mt) outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.0872 time to fit residues: 11.4423 Evaluate side-chains 67 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 54 HIS B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.190385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152585 restraints weight = 6966.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150918 restraints weight = 6859.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.152455 restraints weight = 6222.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.155377 restraints weight = 4268.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155398 restraints weight = 3611.622| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4729 Z= 0.149 Angle : 0.604 10.594 6513 Z= 0.311 Chirality : 0.044 0.127 800 Planarity : 0.003 0.036 863 Dihedral : 9.558 118.174 777 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.41 % Allowed : 24.63 % Favored : 70.96 % 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: 0.25 (0.32), residues: 729 helix: 2.82 (0.33), residues: 262 sheet: -1.09 (0.38), residues: 172 loop : -1.54 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 46 TYR 0.015 0.002 TYR A 325 PHE 0.025 0.002 PHE A 295 TRP 0.020 0.002 TRP B 339 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4729) covalent geometry : angle 0.60443 ( 6513) hydrogen bonds : bond 0.02985 ( 246) hydrogen bonds : angle 4.11300 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8786 (mt) cc_final: 0.8577 (mp) REVERT: A 247 ARG cc_start: 0.8406 (ptm160) cc_final: 0.8030 (ptm160) REVERT: B 14 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8085 (mp) outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 0.0852 time to fit residues: 8.3429 Evaluate side-chains 70 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 50.0000 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 50.0000 chunk 43 optimal weight: 0.0010 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.177919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.140882 restraints weight = 7149.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139618 restraints weight = 7275.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139849 restraints weight = 6504.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140137 restraints weight = 4210.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140762 restraints weight = 3691.025| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 4729 Z= 0.253 Angle : 0.696 10.608 6513 Z= 0.364 Chirality : 0.047 0.137 800 Planarity : 0.004 0.034 863 Dihedral : 9.516 135.522 775 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 8.82 % Allowed : 20.96 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.32), residues: 729 helix: 2.75 (0.33), residues: 264 sheet: -1.76 (0.36), residues: 171 loop : -1.67 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 314 TYR 0.021 0.002 TYR A 325 PHE 0.040 0.004 PHE A 308 TRP 0.025 0.003 TRP B 211 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00587 ( 4729) covalent geometry : angle 0.69571 ( 6513) hydrogen bonds : bond 0.03715 ( 246) hydrogen bonds : angle 4.56634 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.7450 (t80) cc_final: 0.7186 (t80) REVERT: B 210 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7871 (tp) outliers start: 24 outliers final: 16 residues processed: 85 average time/residue: 0.0676 time to fit residues: 7.5804 Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.187825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.152287 restraints weight = 7076.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.149918 restraints weight = 8759.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.151686 restraints weight = 7433.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155331 restraints weight = 4971.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155486 restraints weight = 3568.474| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4729 Z= 0.206 Angle : 0.635 10.913 6513 Z= 0.329 Chirality : 0.045 0.135 800 Planarity : 0.003 0.040 863 Dihedral : 9.382 150.087 775 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 9.19 % Allowed : 24.26 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.32), residues: 729 helix: 2.74 (0.32), residues: 264 sheet: -1.80 (0.37), residues: 169 loop : -1.67 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 46 TYR 0.017 0.002 TYR A 325 PHE 0.049 0.003 PHE A 308 TRP 0.022 0.002 TRP B 211 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 4729) covalent geometry : angle 0.63511 ( 6513) hydrogen bonds : bond 0.03223 ( 246) hydrogen bonds : angle 4.37922 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 255 PHE cc_start: 0.7414 (t80) cc_final: 0.7166 (t80) REVERT: A 274 ASN cc_start: 0.8028 (t0) cc_final: 0.7825 (t0) REVERT: A 312 MET cc_start: 0.6332 (mpp) cc_final: 0.6010 (ptp) REVERT: B 15 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8599 (ttmm) REVERT: B 210 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7920 (tp) outliers start: 25 outliers final: 18 residues processed: 86 average time/residue: 0.0668 time to fit residues: 7.5538 Evaluate side-chains 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 24 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 43 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 60.0000 chunk 34 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.187276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.153260 restraints weight = 7122.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152082 restraints weight = 9535.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.153849 restraints weight = 7290.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.157578 restraints weight = 4914.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.158146 restraints weight = 3285.556| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4729 Z= 0.214 Angle : 0.649 11.864 6513 Z= 0.336 Chirality : 0.045 0.139 800 Planarity : 0.004 0.041 863 Dihedral : 9.588 172.265 775 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 10.29 % Allowed : 23.16 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.32), residues: 729 helix: 2.64 (0.32), residues: 264 sheet: -2.12 (0.36), residues: 163 loop : -1.71 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 27 TYR 0.015 0.002 TYR A 325 PHE 0.039 0.003 PHE A 308 TRP 0.013 0.002 TRP B 169 HIS 0.005 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 4729) covalent geometry : angle 0.64866 ( 6513) hydrogen bonds : bond 0.03377 ( 246) hydrogen bonds : angle 4.40175 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8548 (ttmm) REVERT: B 210 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7931 (tp) outliers start: 28 outliers final: 19 residues processed: 84 average time/residue: 0.0668 time to fit residues: 7.4106 Evaluate side-chains 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 24 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 12 optimal weight: 50.0000 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.188050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.155807 restraints weight = 7254.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.154670 restraints weight = 10376.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156385 restraints weight = 8074.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160106 restraints weight = 5371.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160445 restraints weight = 3527.037| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4729 Z= 0.194 Angle : 0.651 12.744 6513 Z= 0.338 Chirality : 0.045 0.145 800 Planarity : 0.003 0.041 863 Dihedral : 9.371 178.123 775 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 9.19 % Allowed : 26.10 % Favored : 64.71 % 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: -0.33 (0.32), residues: 729 helix: 2.57 (0.32), residues: 264 sheet: -2.07 (0.37), residues: 163 loop : -1.71 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 27 TYR 0.015 0.002 TYR A 325 PHE 0.058 0.003 PHE A 308 TRP 0.012 0.002 TRP B 211 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 4729) covalent geometry : angle 0.65108 ( 6513) hydrogen bonds : bond 0.03172 ( 246) hydrogen bonds : angle 4.45814 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: B 210 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7969 (tp) outliers start: 25 outliers final: 19 residues processed: 85 average time/residue: 0.0624 time to fit residues: 7.0283 Evaluate side-chains 79 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 24 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.192189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.156081 restraints weight = 7016.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151756 restraints weight = 6469.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.152838 restraints weight = 7754.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.154179 restraints weight = 4549.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155093 restraints weight = 3855.218| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4729 Z= 0.114 Angle : 0.583 12.077 6513 Z= 0.303 Chirality : 0.043 0.137 800 Planarity : 0.003 0.041 863 Dihedral : 8.642 172.732 775 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.78 % Allowed : 30.88 % Favored : 64.34 % 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: -0.09 (0.32), residues: 729 helix: 2.69 (0.32), residues: 265 sheet: -1.81 (0.38), residues: 168 loop : -1.58 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 46 TYR 0.007 0.001 TYR A 291 PHE 0.052 0.002 PHE A 308 TRP 0.010 0.002 TRP B 332 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4729) covalent geometry : angle 0.58290 ( 6513) hydrogen bonds : bond 0.02584 ( 246) hydrogen bonds : angle 4.10054 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 312 MET cc_start: 0.6725 (ptp) cc_final: 0.6293 (ptt) REVERT: B 210 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7910 (tp) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.0629 time to fit residues: 7.0259 Evaluate side-chains 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.186869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.152192 restraints weight = 7006.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.152421 restraints weight = 8640.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.153901 restraints weight = 7212.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.154816 restraints weight = 4297.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156410 restraints weight = 3740.247| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4729 Z= 0.193 Angle : 0.651 12.381 6513 Z= 0.335 Chirality : 0.046 0.165 800 Planarity : 0.003 0.042 863 Dihedral : 8.671 173.644 775 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.51 % Allowed : 30.15 % Favored : 64.34 % 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: -0.26 (0.32), residues: 729 helix: 2.58 (0.32), residues: 265 sheet: -1.93 (0.38), residues: 163 loop : -1.70 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.014 0.002 TYR A 325 PHE 0.018 0.002 PHE B 292 TRP 0.028 0.003 TRP B 332 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 4729) covalent geometry : angle 0.65147 ( 6513) hydrogen bonds : bond 0.03087 ( 246) hydrogen bonds : angle 4.32139 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.163 Fit side-chains REVERT: A 312 MET cc_start: 0.6453 (ptp) cc_final: 0.6081 (ptt) REVERT: B 210 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7881 (tp) outliers start: 15 outliers final: 10 residues processed: 74 average time/residue: 0.0654 time to fit residues: 6.4251 Evaluate side-chains 69 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 24 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 50.0000 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.187597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.154263 restraints weight = 7031.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154002 restraints weight = 9771.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.155496 restraints weight = 8498.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156428 restraints weight = 5066.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.157941 restraints weight = 4378.420| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4729 Z= 0.213 Angle : 0.669 12.507 6513 Z= 0.346 Chirality : 0.046 0.144 800 Planarity : 0.003 0.049 863 Dihedral : 8.697 174.166 775 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.88 % Allowed : 30.88 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.35 (0.32), residues: 729 helix: 2.57 (0.32), residues: 265 sheet: -2.03 (0.38), residues: 162 loop : -1.79 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.013 0.002 TYR A 325 PHE 0.017 0.002 PHE B 199 TRP 0.035 0.003 TRP B 339 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 4729) covalent geometry : angle 0.66859 ( 6513) hydrogen bonds : bond 0.03143 ( 246) hydrogen bonds : angle 4.40243 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.148 Fit side-chains REVERT: A 312 MET cc_start: 0.6406 (ptp) cc_final: 0.6091 (ptt) REVERT: B 210 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7897 (tp) outliers start: 16 outliers final: 11 residues processed: 73 average time/residue: 0.0670 time to fit residues: 6.4467 Evaluate side-chains 70 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.195564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144173 restraints weight = 6839.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147364 restraints weight = 4883.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.149145 restraints weight = 3902.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149722 restraints weight = 3467.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150387 restraints weight = 3094.542| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4729 Z= 0.246 Angle : 0.697 12.187 6513 Z= 0.362 Chirality : 0.047 0.180 800 Planarity : 0.004 0.051 863 Dihedral : 8.911 179.013 775 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.51 % Allowed : 30.51 % Favored : 63.97 % 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: -0.50 (0.32), residues: 729 helix: 2.51 (0.32), residues: 264 sheet: -2.14 (0.38), residues: 167 loop : -1.89 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 49 TYR 0.014 0.002 TYR A 325 PHE 0.030 0.002 PHE B 292 TRP 0.021 0.003 TRP B 339 HIS 0.004 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 4729) covalent geometry : angle 0.69697 ( 6513) hydrogen bonds : bond 0.03388 ( 246) hydrogen bonds : angle 4.61265 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.171 Fit side-chains REVERT: A 294 GLU cc_start: 0.6370 (mp0) cc_final: 0.6141 (mp0) REVERT: A 312 MET cc_start: 0.7025 (ptp) cc_final: 0.6725 (ptt) REVERT: B 210 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7930 (tp) REVERT: B 300 LEU cc_start: 0.8377 (mt) cc_final: 0.7831 (mp) REVERT: G 32 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8641 (mmmt) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.0573 time to fit residues: 5.7863 Evaluate side-chains 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 chunk 28 optimal weight: 0.0020 overall best weight: 0.8390 ------------------------------------------------------------------------------- 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 = 0.4504 r_free = 0.4504 target = 0.197805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.160035 restraints weight = 6722.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.157757 restraints weight = 7454.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.159877 restraints weight = 6363.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.160631 restraints weight = 4532.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162088 restraints weight = 4233.029| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4729 Z= 0.124 Angle : 0.610 12.367 6513 Z= 0.313 Chirality : 0.044 0.179 800 Planarity : 0.003 0.055 863 Dihedral : 8.346 173.624 775 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.31 % Allowed : 33.09 % Favored : 63.60 % 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: -0.30 (0.32), residues: 729 helix: 2.68 (0.32), residues: 265 sheet: -1.99 (0.37), residues: 176 loop : -1.80 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.008 0.001 TYR B 85 PHE 0.019 0.001 PHE B 292 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4729) covalent geometry : angle 0.61020 ( 6513) hydrogen bonds : bond 0.02587 ( 246) hydrogen bonds : angle 4.21423 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 864.30 seconds wall clock time: 15 minutes 30.81 seconds (930.81 seconds total)