Starting phenix.real_space_refine on Fri Aug 22 19:54:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qot_18541/08_2025/8qot_18541.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qot_18541/08_2025/8qot_18541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qot_18541/08_2025/8qot_18541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qot_18541/08_2025/8qot_18541.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qot_18541/08_2025/8qot_18541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qot_18541/08_2025/8qot_18541.map" } resolution = 3.2 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 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4791 2.51 5 N 1243 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7493 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2320 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Conformer: "B" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} bond proxies already assigned to first conformer: 2355 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 948 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1708 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "L" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1586 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198} Chain: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 931 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 320 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 320 " occ=0.50 Time building chain proxies: 2.82, per 1000 atoms: 0.38 Number of scatterers: 7493 At special positions: 0 Unit cell: (66.3612, 89.7828, 161.999, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1416 8.00 N 1243 7.00 C 4791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.05 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: 0.67 Conformation dependent library (CDL) restraints added in 593.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1802 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 18 sheets defined 30.2% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 66 through 95 Processing helix chain 'A' and resid 101 through 131 Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 136 through 170 removed outlier: 3.676A pdb=" N CYS A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 180 through 205 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 224 through 258 removed outlier: 3.735A pdb=" N TRP A 228 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.863A pdb=" N MET A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 306 removed outlier: 3.786A pdb=" N LEU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Proline residue: A 295 - end of helix Processing helix chain 'A' and resid 311 through 339 removed outlier: 3.793A pdb=" N SER A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS A 330 " --> pdb=" O TYR A 326 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 341 through 350 removed outlier: 4.250A pdb=" N GLU A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.810A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.514A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100C Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.688A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.676A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.855A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.532A pdb=" N THR A 218 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.786A pdb=" N SER B 9 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.167A pdb=" N GLY B 12 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.167A pdb=" N GLY B 12 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.679A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.998A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR H 50 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.753A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.753A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.609A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.553A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 Processing sheet with id=AB4, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.627A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.601A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.859A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.636A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE K 94 " --> pdb=" O TYR K 102 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR K 102 " --> pdb=" O ILE K 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.636A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2338 1.35 - 1.47: 2075 1.47 - 1.59: 3200 1.59 - 1.71: 0 1.71 - 1.83: 61 Bond restraints: 7674 Sorted by residual: bond pdb=" N VAL K 69 " pdb=" CA VAL K 69 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.14e-02 7.69e+03 6.73e+00 bond pdb=" CA SER K 70 " pdb=" CB SER K 70 " ideal model delta sigma weight residual 1.533 1.492 0.041 1.69e-02 3.50e+03 5.97e+00 bond pdb=" N SER K 70 " pdb=" CA SER K 70 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.20e-02 6.94e+03 5.68e+00 bond pdb=" N ARG K 71 " pdb=" CA ARG K 71 " ideal model delta sigma weight residual 1.455 1.482 -0.026 1.22e-02 6.72e+03 4.66e+00 bond pdb=" N ASP K 72 " pdb=" CA ASP K 72 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.27e-02 6.20e+03 4.45e+00 ... (remaining 7669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 10124 1.57 - 3.14: 254 3.14 - 4.70: 45 4.70 - 6.27: 10 6.27 - 7.84: 1 Bond angle restraints: 10434 Sorted by residual: angle pdb=" CA ARG A 258 " pdb=" CB ARG A 258 " pdb=" CG ARG A 258 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" N THR H 160 " pdb=" CA THR H 160 " pdb=" C THR H 160 " ideal model delta sigma weight residual 114.56 110.30 4.26 1.27e+00 6.20e-01 1.12e+01 angle pdb=" C LEU A 257 " pdb=" N ARG A 258 " pdb=" CA ARG A 258 " ideal model delta sigma weight residual 122.73 117.58 5.15 1.61e+00 3.86e-01 1.02e+01 angle pdb=" CA ARG K 71 " pdb=" C ARG K 71 " pdb=" O ARG K 71 " ideal model delta sigma weight residual 120.80 117.88 2.92 1.11e+00 8.12e-01 6.94e+00 angle pdb=" CA VAL K 69 " pdb=" C VAL K 69 " pdb=" O VAL K 69 " ideal model delta sigma weight residual 120.67 117.65 3.02 1.17e+00 7.31e-01 6.64e+00 ... (remaining 10429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4182 17.98 - 35.95: 279 35.95 - 53.93: 46 53.93 - 71.90: 7 71.90 - 89.88: 8 Dihedral angle restraints: 4522 sinusoidal: 1698 harmonic: 2824 Sorted by residual: dihedral pdb=" CA ARG A 95 " pdb=" C ARG A 95 " pdb=" N TYR A 96 " pdb=" CA TYR A 96 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 54.46 38.54 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA LYS A 100 " pdb=" C LYS A 100 " pdb=" N THR A 101 " pdb=" CA THR A 101 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 781 0.037 - 0.074: 292 0.074 - 0.111: 80 0.111 - 0.148: 23 0.148 - 0.186: 3 Chirality restraints: 1179 Sorted by residual: chirality pdb=" CA ARG A 258 " pdb=" N ARG A 258 " pdb=" C ARG A 258 " pdb=" CB ARG A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA VAL K 69 " pdb=" N VAL K 69 " pdb=" C VAL K 69 " pdb=" CB VAL K 69 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CB THR B 35 " pdb=" CA THR B 35 " pdb=" OG1 THR B 35 " pdb=" CG2 THR B 35 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1176 not shown) Planarity restraints: 1304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 238 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ILE A 238 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 238 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 239 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 239 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C PHE A 239 " 0.027 2.00e-02 2.50e+03 pdb=" O PHE A 239 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 240 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 71 " 0.136 9.50e-02 1.11e+02 6.10e-02 2.29e+00 pdb=" NE ARG K 71 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG K 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG K 71 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 71 " 0.005 2.00e-02 2.50e+03 ... (remaining 1301 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1004 2.76 - 3.29: 6956 3.29 - 3.83: 11499 3.83 - 4.36: 12874 4.36 - 4.90: 23368 Nonbonded interactions: 55701 Sorted by model distance: nonbonded pdb=" O ILE A 290 " pdb=" OG1 THR A 294 " model vdw 2.219 3.040 nonbonded pdb=" O PRO A 122 " pdb=" OG SER A 125 " model vdw 2.256 3.040 nonbonded pdb=" ND2 ASN H 100H" pdb=" O ALA L 32 " model vdw 2.292 3.120 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.299 3.040 nonbonded pdb=" O LYS A 100 " pdb=" OG1 THR A 101 " model vdw 2.304 3.040 ... (remaining 55696 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=0.50 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.570 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 0.045 7681 Z= 0.195 Angle : 0.626 7.838 10448 Z= 0.344 Chirality : 0.043 0.186 1179 Planarity : 0.004 0.061 1304 Dihedral : 12.782 89.878 2699 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.08 (0.26), residues: 959 helix: 1.34 (0.31), residues: 247 sheet: 0.33 (0.30), residues: 292 loop : -0.89 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 258 TYR 0.024 0.002 TYR L 55 PHE 0.021 0.002 PHE L 118 TRP 0.018 0.001 TRP H 99 HIS 0.003 0.001 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7674) covalent geometry : angle 0.62433 (10434) SS BOND : bond 0.00709 ( 7) SS BOND : angle 1.45362 ( 14) hydrogen bonds : bond 0.22505 ( 383) hydrogen bonds : angle 8.18482 ( 1141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.291 Fit side-chains REVERT: A 158 LEU cc_start: 0.8111 (tp) cc_final: 0.7898 (tt) REVERT: L 82 ASP cc_start: 0.7321 (m-30) cc_final: 0.7048 (m-30) REVERT: K 100 TYR cc_start: 0.8840 (m-80) cc_final: 0.8629 (m-80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0970 time to fit residues: 25.1901 Evaluate side-chains 154 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN L 124 GLN L 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109380 restraints weight = 26559.077| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 4.88 r_work: 0.3248 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7681 Z= 0.196 Angle : 0.664 10.514 10448 Z= 0.351 Chirality : 0.044 0.160 1179 Planarity : 0.004 0.030 1304 Dihedral : 4.663 26.595 1061 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.57 % Allowed : 10.64 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.43 (0.27), residues: 959 helix: 1.39 (0.32), residues: 247 sheet: 0.84 (0.29), residues: 313 loop : -0.86 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 258 TYR 0.018 0.002 TYR L 140 PHE 0.021 0.002 PHE A 108 TRP 0.012 0.001 TRP H 99 HIS 0.005 0.001 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 7674) covalent geometry : angle 0.66263 (10434) SS BOND : bond 0.00808 ( 7) SS BOND : angle 1.46186 ( 14) hydrogen bonds : bond 0.05372 ( 383) hydrogen bonds : angle 6.02048 ( 1141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8121 (tp) cc_final: 0.7920 (tt) REVERT: A 205 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7479 (ttm) REVERT: A 336 TYR cc_start: 0.8452 (m-80) cc_final: 0.8154 (m-80) REVERT: B 102 TYR cc_start: 0.8084 (m-80) cc_final: 0.7804 (m-80) REVERT: L 82 ASP cc_start: 0.8128 (m-30) cc_final: 0.7642 (m-30) REVERT: K 34 MET cc_start: 0.8645 (mmm) cc_final: 0.8126 (mmm) REVERT: K 82 ASN cc_start: 0.8449 (m-40) cc_final: 0.8245 (m110) REVERT: K 96 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8617 (p) REVERT: K 100 TYR cc_start: 0.8985 (m-80) cc_final: 0.8723 (m-80) outliers start: 13 outliers final: 8 residues processed: 162 average time/residue: 0.0731 time to fit residues: 15.7753 Evaluate side-chains 157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 96 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 48 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 80 optimal weight: 0.0040 chunk 41 optimal weight: 0.9980 overall best weight: 0.1306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111667 restraints weight = 23847.759| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.64 r_work: 0.3298 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7681 Z= 0.112 Angle : 0.590 10.415 10448 Z= 0.306 Chirality : 0.041 0.140 1179 Planarity : 0.004 0.045 1304 Dihedral : 4.280 26.604 1061 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.81 % Allowed : 12.70 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.80 (0.27), residues: 959 helix: 1.63 (0.33), residues: 247 sheet: 1.22 (0.29), residues: 313 loop : -0.74 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 258 TYR 0.018 0.001 TYR L 140 PHE 0.019 0.001 PHE H 146 TRP 0.011 0.001 TRP H 99 HIS 0.002 0.000 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7674) covalent geometry : angle 0.58837 (10434) SS BOND : bond 0.00457 ( 7) SS BOND : angle 1.26783 ( 14) hydrogen bonds : bond 0.04112 ( 383) hydrogen bonds : angle 5.37477 ( 1141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.257 Fit side-chains REVERT: A 133 TRP cc_start: 0.8375 (t-100) cc_final: 0.7994 (t-100) REVERT: A 255 MET cc_start: 0.5616 (mmt) cc_final: 0.4682 (mmp) REVERT: A 336 TYR cc_start: 0.8472 (m-80) cc_final: 0.8217 (m-80) REVERT: B 99 PHE cc_start: 0.8153 (t80) cc_final: 0.7891 (t80) REVERT: B 102 TYR cc_start: 0.8132 (m-80) cc_final: 0.7865 (m-80) REVERT: H 83 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7388 (mtm-85) REVERT: H 171 GLN cc_start: 0.8560 (mt0) cc_final: 0.7949 (mt0) REVERT: H 177 SER cc_start: 0.8832 (p) cc_final: 0.8386 (m) REVERT: L 42 LYS cc_start: 0.8690 (mmtm) cc_final: 0.8452 (mmmm) REVERT: L 81 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7510 (tm-30) REVERT: L 82 ASP cc_start: 0.8064 (m-30) cc_final: 0.7462 (m-30) REVERT: L 161 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8270 (mt-10) REVERT: K 34 MET cc_start: 0.8600 (mmm) cc_final: 0.8133 (mmm) outliers start: 15 outliers final: 10 residues processed: 166 average time/residue: 0.0711 time to fit residues: 15.6949 Evaluate side-chains 166 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109284 restraints weight = 20257.293| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.18 r_work: 0.3274 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7681 Z= 0.169 Angle : 0.613 9.569 10448 Z= 0.320 Chirality : 0.042 0.234 1179 Planarity : 0.004 0.043 1304 Dihedral : 4.434 27.409 1061 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.30 % Allowed : 14.03 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.75 (0.27), residues: 959 helix: 1.49 (0.33), residues: 248 sheet: 1.21 (0.28), residues: 326 loop : -0.80 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 258 TYR 0.017 0.001 TYR K 100 PHE 0.020 0.002 PHE A 338 TRP 0.015 0.001 TRP H 99 HIS 0.004 0.001 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7674) covalent geometry : angle 0.61140 (10434) SS BOND : bond 0.00659 ( 7) SS BOND : angle 1.46719 ( 14) hydrogen bonds : bond 0.04369 ( 383) hydrogen bonds : angle 5.31907 ( 1141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.231 Fit side-chains REVERT: A 133 TRP cc_start: 0.8407 (t-100) cc_final: 0.8043 (t-100) REVERT: A 153 THR cc_start: 0.7256 (m) cc_final: 0.7014 (p) REVERT: A 336 TYR cc_start: 0.8440 (m-80) cc_final: 0.8159 (m-80) REVERT: B 102 TYR cc_start: 0.8148 (m-80) cc_final: 0.7850 (m-80) REVERT: H 83 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7509 (mtm-85) REVERT: H 116 THR cc_start: 0.8335 (m) cc_final: 0.7914 (t) REVERT: H 171 GLN cc_start: 0.8661 (mt0) cc_final: 0.8026 (mt0) REVERT: H 177 SER cc_start: 0.8875 (p) cc_final: 0.8405 (m) REVERT: L 81 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7500 (tm-30) REVERT: L 82 ASP cc_start: 0.8103 (m-30) cc_final: 0.7497 (m-30) REVERT: K 34 MET cc_start: 0.8537 (mmm) cc_final: 0.8035 (mmm) REVERT: K 35 SER cc_start: 0.8264 (m) cc_final: 0.7858 (p) REVERT: K 70 SER cc_start: 0.8672 (t) cc_final: 0.7968 (p) outliers start: 19 outliers final: 14 residues processed: 167 average time/residue: 0.0628 time to fit residues: 14.3331 Evaluate side-chains 168 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107128 restraints weight = 29659.595| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 5.25 r_work: 0.3212 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7681 Z= 0.148 Angle : 0.594 10.342 10448 Z= 0.311 Chirality : 0.042 0.188 1179 Planarity : 0.004 0.042 1304 Dihedral : 4.422 28.012 1061 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.54 % Allowed : 15.60 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.81 (0.27), residues: 959 helix: 1.59 (0.33), residues: 248 sheet: 1.28 (0.28), residues: 334 loop : -0.90 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 258 TYR 0.019 0.001 TYR L 140 PHE 0.022 0.001 PHE A 338 TRP 0.010 0.001 TRP A 226 HIS 0.004 0.001 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7674) covalent geometry : angle 0.59240 (10434) SS BOND : bond 0.00583 ( 7) SS BOND : angle 1.39934 ( 14) hydrogen bonds : bond 0.04115 ( 383) hydrogen bonds : angle 5.15902 ( 1141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.162 Fit side-chains REVERT: A 133 TRP cc_start: 0.8465 (t-100) cc_final: 0.8004 (t-100) REVERT: A 153 THR cc_start: 0.7390 (m) cc_final: 0.7176 (p) REVERT: A 158 LEU cc_start: 0.8030 (tp) cc_final: 0.7820 (tt) REVERT: A 336 TYR cc_start: 0.8499 (m-80) cc_final: 0.7959 (m-80) REVERT: B 102 TYR cc_start: 0.8200 (m-80) cc_final: 0.7978 (m-80) REVERT: H 83 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7594 (mtm-85) REVERT: H 116 THR cc_start: 0.8389 (m) cc_final: 0.7996 (t) REVERT: H 171 GLN cc_start: 0.8692 (mt0) cc_final: 0.8053 (mt0) REVERT: H 177 SER cc_start: 0.8909 (p) cc_final: 0.8428 (m) REVERT: L 81 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7598 (tm-30) REVERT: L 82 ASP cc_start: 0.8194 (m-30) cc_final: 0.7586 (m-30) REVERT: L 161 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8282 (mt-10) REVERT: L 187 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: K 34 MET cc_start: 0.8599 (mmm) cc_final: 0.8103 (mmm) REVERT: K 35 SER cc_start: 0.8322 (m) cc_final: 0.8055 (t) REVERT: K 97 ASP cc_start: 0.8974 (t0) cc_final: 0.8689 (t70) outliers start: 21 outliers final: 15 residues processed: 163 average time/residue: 0.0688 time to fit residues: 15.3788 Evaluate side-chains 166 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN H 35 HIS H 197 ASN L 198 HIS K 82AASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.134604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105034 restraints weight = 23456.403| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.49 r_work: 0.3194 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7681 Z= 0.265 Angle : 0.679 10.504 10448 Z= 0.358 Chirality : 0.045 0.194 1179 Planarity : 0.004 0.039 1304 Dihedral : 4.851 29.405 1061 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.78 % Allowed : 15.48 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.51 (0.27), residues: 959 helix: 1.24 (0.32), residues: 246 sheet: 1.28 (0.29), residues: 317 loop : -1.07 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 258 TYR 0.018 0.002 TYR K 100 PHE 0.020 0.002 PHE A 108 TRP 0.012 0.002 TRP A 226 HIS 0.008 0.002 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 7674) covalent geometry : angle 0.67574 (10434) SS BOND : bond 0.00746 ( 7) SS BOND : angle 1.85153 ( 14) hydrogen bonds : bond 0.05025 ( 383) hydrogen bonds : angle 5.48987 ( 1141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.212 Fit side-chains REVERT: A 90 MET cc_start: 0.6676 (mmp) cc_final: 0.6250 (mmp) REVERT: A 153 THR cc_start: 0.7395 (m) cc_final: 0.7127 (p) REVERT: A 158 LEU cc_start: 0.8169 (tp) cc_final: 0.7958 (tt) REVERT: A 255 MET cc_start: 0.5596 (mmt) cc_final: 0.5345 (mmp) REVERT: A 336 TYR cc_start: 0.8527 (m-80) cc_final: 0.7899 (m-80) REVERT: B 4 VAL cc_start: 0.7824 (t) cc_final: 0.7606 (t) REVERT: H 83 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7723 (ptp-110) REVERT: H 116 THR cc_start: 0.8481 (m) cc_final: 0.8157 (t) REVERT: H 171 GLN cc_start: 0.8683 (mt0) cc_final: 0.8068 (mt0) REVERT: H 177 SER cc_start: 0.8925 (p) cc_final: 0.8395 (m) REVERT: L 81 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7620 (tm-30) REVERT: L 82 ASP cc_start: 0.8175 (m-30) cc_final: 0.7617 (m-30) REVERT: L 187 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: K 34 MET cc_start: 0.8555 (mmm) cc_final: 0.8237 (mpp) REVERT: K 97 ASP cc_start: 0.8953 (t0) cc_final: 0.8744 (t70) outliers start: 23 outliers final: 20 residues processed: 160 average time/residue: 0.0685 time to fit residues: 14.7506 Evaluate side-chains 168 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 46 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 44 optimal weight: 0.0020 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.136625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105705 restraints weight = 30782.361| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 5.28 r_work: 0.3186 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7681 Z= 0.144 Angle : 0.609 10.392 10448 Z= 0.316 Chirality : 0.042 0.170 1179 Planarity : 0.004 0.041 1304 Dihedral : 4.558 29.286 1061 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.90 % Allowed : 15.84 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.66 (0.27), residues: 959 helix: 1.55 (0.33), residues: 248 sheet: 1.26 (0.29), residues: 325 loop : -1.05 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 258 TYR 0.018 0.001 TYR K 100 PHE 0.020 0.002 PHE H 146 TRP 0.008 0.001 TRP A 226 HIS 0.003 0.001 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7674) covalent geometry : angle 0.60769 (10434) SS BOND : bond 0.00543 ( 7) SS BOND : angle 1.41549 ( 14) hydrogen bonds : bond 0.04226 ( 383) hydrogen bonds : angle 5.15360 ( 1141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.7388 (m) cc_final: 0.7170 (p) REVERT: A 158 LEU cc_start: 0.8133 (tp) cc_final: 0.7920 (tt) REVERT: A 303 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7835 (mmtp) REVERT: A 336 TYR cc_start: 0.8517 (m-80) cc_final: 0.7914 (m-80) REVERT: B 102 TYR cc_start: 0.8198 (m-80) cc_final: 0.7963 (m-80) REVERT: H 83 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7750 (ptp-110) REVERT: H 116 THR cc_start: 0.8449 (m) cc_final: 0.8097 (t) REVERT: L 81 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7685 (tm-30) REVERT: L 82 ASP cc_start: 0.8199 (m-30) cc_final: 0.7692 (m-30) REVERT: L 187 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: K 34 MET cc_start: 0.8573 (mmm) cc_final: 0.8288 (mpp) REVERT: K 97 ASP cc_start: 0.8957 (t0) cc_final: 0.8674 (t70) outliers start: 24 outliers final: 17 residues processed: 156 average time/residue: 0.0845 time to fit residues: 17.8456 Evaluate side-chains 163 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.137402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107176 restraints weight = 26381.202| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.79 r_work: 0.3220 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7681 Z= 0.142 Angle : 0.612 10.598 10448 Z= 0.315 Chirality : 0.042 0.191 1179 Planarity : 0.004 0.047 1304 Dihedral : 4.477 29.203 1061 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.66 % Allowed : 16.69 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.74 (0.27), residues: 959 helix: 1.58 (0.33), residues: 249 sheet: 1.28 (0.29), residues: 329 loop : -1.00 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 258 TYR 0.019 0.001 TYR K 100 PHE 0.020 0.001 PHE A 350 TRP 0.008 0.001 TRP H 99 HIS 0.003 0.001 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7674) covalent geometry : angle 0.60992 (10434) SS BOND : bond 0.00557 ( 7) SS BOND : angle 1.35590 ( 14) hydrogen bonds : bond 0.04097 ( 383) hydrogen bonds : angle 5.06575 ( 1141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.171 Fit side-chains REVERT: A 158 LEU cc_start: 0.8085 (tp) cc_final: 0.7879 (tt) REVERT: A 303 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7829 (mmtp) REVERT: A 336 TYR cc_start: 0.8440 (m-80) cc_final: 0.7939 (m-80) REVERT: B 102 TYR cc_start: 0.8145 (m-80) cc_final: 0.7871 (m-80) REVERT: H 83 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7737 (ptp-110) REVERT: H 116 THR cc_start: 0.8443 (m) cc_final: 0.8079 (t) REVERT: H 171 GLN cc_start: 0.8699 (mt0) cc_final: 0.8342 (mt0) REVERT: H 177 SER cc_start: 0.8989 (p) cc_final: 0.8723 (m) REVERT: L 81 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7629 (tm-30) REVERT: L 82 ASP cc_start: 0.8168 (m-30) cc_final: 0.7638 (m-30) REVERT: L 161 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8285 (mt-10) REVERT: L 187 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: K 34 MET cc_start: 0.8497 (mmm) cc_final: 0.8235 (mpp) REVERT: K 97 ASP cc_start: 0.8968 (t0) cc_final: 0.8638 (t70) outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 0.0750 time to fit residues: 16.0222 Evaluate side-chains 166 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.0170 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 chunk 61 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108864 restraints weight = 25640.570| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.74 r_work: 0.3249 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7681 Z= 0.114 Angle : 0.599 11.221 10448 Z= 0.306 Chirality : 0.041 0.221 1179 Planarity : 0.003 0.040 1304 Dihedral : 4.209 28.361 1061 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.18 % Allowed : 17.53 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.92 (0.27), residues: 959 helix: 1.75 (0.33), residues: 249 sheet: 1.45 (0.29), residues: 321 loop : -0.92 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 258 TYR 0.017 0.001 TYR K 100 PHE 0.027 0.001 PHE A 338 TRP 0.007 0.001 TRP A 133 HIS 0.001 0.000 HIS H 200 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7674) covalent geometry : angle 0.59761 (10434) SS BOND : bond 0.00456 ( 7) SS BOND : angle 1.16325 ( 14) hydrogen bonds : bond 0.03667 ( 383) hydrogen bonds : angle 4.85428 ( 1141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8044 (tp) cc_final: 0.7816 (tt) REVERT: A 336 TYR cc_start: 0.8210 (m-80) cc_final: 0.7817 (m-80) REVERT: B 102 TYR cc_start: 0.8184 (m-80) cc_final: 0.7973 (m-80) REVERT: H 83 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7571 (mtm-85) REVERT: H 116 THR cc_start: 0.8397 (m) cc_final: 0.8051 (t) REVERT: L 42 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8453 (mmmm) REVERT: L 79 GLN cc_start: 0.8626 (mm110) cc_final: 0.8220 (mm-40) REVERT: L 81 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7669 (tm-30) REVERT: L 82 ASP cc_start: 0.8127 (m-30) cc_final: 0.7634 (m-30) REVERT: L 161 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8198 (mt-10) REVERT: L 187 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: K 34 MET cc_start: 0.8500 (mmm) cc_final: 0.8254 (mpp) REVERT: K 82 MET cc_start: 0.7432 (ptp) cc_final: 0.7189 (ptp) REVERT: K 97 ASP cc_start: 0.8966 (t0) cc_final: 0.8708 (t70) outliers start: 18 outliers final: 15 residues processed: 155 average time/residue: 0.0922 time to fit residues: 19.3811 Evaluate side-chains 157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 45 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 0.0170 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107478 restraints weight = 30713.647| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 5.29 r_work: 0.3211 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7681 Z= 0.131 Angle : 0.628 11.220 10448 Z= 0.318 Chirality : 0.042 0.226 1179 Planarity : 0.004 0.038 1304 Dihedral : 4.259 28.975 1061 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.93 % Allowed : 18.50 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.92 (0.27), residues: 959 helix: 1.69 (0.33), residues: 249 sheet: 1.49 (0.29), residues: 321 loop : -0.91 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 258 TYR 0.019 0.001 TYR K 100 PHE 0.024 0.001 PHE A 338 TRP 0.015 0.001 TRP A 192 HIS 0.003 0.001 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7674) covalent geometry : angle 0.62650 (10434) SS BOND : bond 0.00514 ( 7) SS BOND : angle 1.16840 ( 14) hydrogen bonds : bond 0.03816 ( 383) hydrogen bonds : angle 4.88856 ( 1141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.292 Fit side-chains REVERT: A 158 LEU cc_start: 0.8080 (tp) cc_final: 0.7831 (tt) REVERT: A 336 TYR cc_start: 0.8191 (m-80) cc_final: 0.7707 (m-10) REVERT: B 102 TYR cc_start: 0.8218 (m-80) cc_final: 0.7986 (m-80) REVERT: H 83 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7576 (mtm-85) REVERT: H 116 THR cc_start: 0.8442 (m) cc_final: 0.8102 (t) REVERT: H 177 SER cc_start: 0.8992 (p) cc_final: 0.8546 (m) REVERT: L 42 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8467 (mmmm) REVERT: L 81 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7714 (tm-30) REVERT: L 82 ASP cc_start: 0.8185 (m-30) cc_final: 0.7703 (m-30) REVERT: L 161 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8254 (mt-10) REVERT: L 187 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: K 34 MET cc_start: 0.8538 (mmm) cc_final: 0.8289 (mpp) REVERT: K 82 MET cc_start: 0.7501 (ptp) cc_final: 0.7299 (ptp) REVERT: K 97 ASP cc_start: 0.8990 (t0) cc_final: 0.8722 (t70) outliers start: 16 outliers final: 13 residues processed: 150 average time/residue: 0.0911 time to fit residues: 18.5298 Evaluate side-chains 157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.137724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108289 restraints weight = 23691.526| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.48 r_work: 0.3247 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7681 Z= 0.143 Angle : 0.630 11.140 10448 Z= 0.320 Chirality : 0.042 0.221 1179 Planarity : 0.003 0.038 1304 Dihedral : 4.339 29.089 1061 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.06 % Allowed : 18.86 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 aren not related in a simple way. whole: 0.89 (0.27), residues: 959 helix: 1.65 (0.33), residues: 249 sheet: 1.50 (0.29), residues: 322 loop : -0.95 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 258 TYR 0.019 0.001 TYR K 100 PHE 0.025 0.001 PHE A 338 TRP 0.011 0.001 TRP A 192 HIS 0.003 0.001 HIS H 164 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7674) covalent geometry : angle 0.62851 (10434) SS BOND : bond 0.00543 ( 7) SS BOND : angle 1.22475 ( 14) hydrogen bonds : bond 0.03937 ( 383) hydrogen bonds : angle 4.95016 ( 1141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.26 seconds wall clock time: 33 minutes 7.62 seconds (1987.62 seconds total)