Starting phenix.real_space_refine on Wed Sep 17 08:42:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jg0_61446/09_2025/9jg0_61446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jg0_61446/09_2025/9jg0_61446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jg0_61446/09_2025/9jg0_61446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jg0_61446/09_2025/9jg0_61446.map" model { file = "/net/cci-nas-00/data/ceres_data/9jg0_61446/09_2025/9jg0_61446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jg0_61446/09_2025/9jg0_61446.cif" } resolution = 2.91 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= -0.002 sd= 0.115 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 35 5.16 5 C 4663 2.51 5 N 1216 2.21 5 O 1357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7271 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3076 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 13, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "H" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 10, 'TRANS': 201} Time building chain proxies: 1.99, per 1000 atoms: 0.27 Number of scatterers: 7271 At special positions: 0 Unit cell: (66.15, 100.8, 152.25, 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 35 16.00 O 1357 8.00 N 1216 7.00 C 4663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 206 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 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: 0.54 Conformation dependent library (CDL) restraints added in 423.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1784 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 40.9% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 41 through 73 Processing helix chain 'R' and resid 78 through 98 Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 114 through 149 Processing helix chain 'R' and resid 156 through 175 Processing helix chain 'R' and resid 175 through 181 removed outlier: 4.350A pdb=" N ALA R 179 " --> pdb=" O MET R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 228 removed outlier: 3.620A pdb=" N ARG R 216 " --> pdb=" O ASN R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 270 removed outlier: 3.841A pdb=" N LEU R 250 " --> pdb=" O ALA R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 293 removed outlier: 3.736A pdb=" N VAL R 276 " --> pdb=" O ASN R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 332 removed outlier: 3.518A pdb=" N PHE R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 343 Processing helix chain 'R' and resid 343 through 352 removed outlier: 3.788A pdb=" N THR R 347 " --> pdb=" O GLN R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 396 removed outlier: 3.672A pdb=" N LEU R 363 " --> pdb=" O ALA R 359 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS R 368 " --> pdb=" O ARG R 364 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE R 369 " --> pdb=" O LYS R 365 " (cutoff:3.500A) Proline residue: R 386 - end of helix Processing helix chain 'R' and resid 400 through 411 Processing helix chain 'R' and resid 411 through 422 Processing helix chain 'R' and resid 425 through 433 Processing helix chain 'R' and resid 434 through 449 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.884A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 200 through 206 removed outlier: 4.133A pdb=" N GLY H 204 " --> pdb=" O SER H 200 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.685A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.105A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 185 through 190 removed outlier: 3.619A pdb=" N LYS L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 33 through 36 removed outlier: 6.099A pdb=" N THR R 33 " --> pdb=" O ARG R 191 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG R 193 " --> pdb=" O THR R 33 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL R 35 " --> pdb=" O ARG R 193 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS R 183 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG R 207 " --> pdb=" O HIS R 183 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL R 203 " --> pdb=" O GLU R 187 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N TYR R 189 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N SER R 201 " --> pdb=" O TYR R 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'H' and resid 14 through 15 removed outlier: 8.726A pdb=" N PHE H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER H 55 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 14 through 15 removed outlier: 4.440A pdb=" N TYR H 116 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.504A pdb=" N LYS H 157 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.504A pdb=" N LYS H 157 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.156A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.527A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLY K 16 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 10 through 11 removed outlier: 5.633A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP K 99 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 10 through 11 removed outlier: 5.633A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE K 98 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.480A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.480A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU L 93 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU L 97 " --> pdb=" O LEU L 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.009A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 147 through 152 456 hydrogen bonds defined for protein. 1278 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: 1.29 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2297 1.34 - 1.46: 1746 1.46 - 1.58: 3342 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 7439 Sorted by residual: bond pdb=" C SER R 176 " pdb=" N PRO R 177 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.28e-02 6.10e+03 9.73e-01 bond pdb=" CB ARG H 101 " pdb=" CG ARG H 101 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" C MET R 99 " pdb=" N PRO R 100 " ideal model delta sigma weight residual 1.335 1.343 -0.009 1.28e-02 6.10e+03 4.81e-01 bond pdb=" CA SER L 8 " pdb=" C SER L 8 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 4.44e-01 bond pdb=" CB VAL R 94 " pdb=" CG2 VAL R 94 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.42e-01 ... (remaining 7434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 9963 1.58 - 3.15: 128 3.15 - 4.73: 25 4.73 - 6.31: 4 6.31 - 7.88: 2 Bond angle restraints: 10122 Sorted by residual: angle pdb=" CA LEU L 97 " pdb=" CB LEU L 97 " pdb=" CG LEU L 97 " ideal model delta sigma weight residual 116.30 124.18 -7.88 3.50e+00 8.16e-02 5.07e+00 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.55e+00 angle pdb=" C ILE R 174 " pdb=" N MET R 175 " pdb=" CA MET R 175 " ideal model delta sigma weight residual 122.50 118.84 3.66 1.82e+00 3.02e-01 4.04e+00 angle pdb=" C VAL L 134 " pdb=" N VAL L 135 " pdb=" CA VAL L 135 " ideal model delta sigma weight residual 122.99 120.24 2.75 1.39e+00 5.18e-01 3.91e+00 angle pdb=" CA GLY K 16 " pdb=" C GLY K 16 " pdb=" O GLY K 16 " ideal model delta sigma weight residual 122.47 120.34 2.13 1.08e+00 8.57e-01 3.89e+00 ... (remaining 10117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3975 17.96 - 35.92: 328 35.92 - 53.88: 83 53.88 - 71.84: 14 71.84 - 89.80: 9 Dihedral angle restraints: 4409 sinusoidal: 1638 harmonic: 2771 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 33.78 59.22 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 136.22 -43.22 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual 93.00 57.66 35.34 1 1.00e+01 1.00e-02 1.77e+01 ... (remaining 4406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 661 0.029 - 0.058: 328 0.058 - 0.087: 108 0.087 - 0.117: 49 0.117 - 0.146: 10 Chirality restraints: 1156 Sorted by residual: chirality pdb=" CA VAL H 40 " pdb=" N VAL H 40 " pdb=" C VAL H 40 " pdb=" CB VAL H 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CB ILE K 98 " pdb=" CA ILE K 98 " pdb=" CG1 ILE K 98 " pdb=" CG2 ILE K 98 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE H 209 " pdb=" N ILE H 209 " pdb=" C ILE H 209 " pdb=" CB ILE H 209 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1153 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 176 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO R 177 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 177 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 177 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO H 109 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 149 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.37e-01 pdb=" N PRO R 150 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO R 150 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 150 " -0.014 5.00e-02 4.00e+02 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1316 2.77 - 3.30: 6852 3.30 - 3.84: 12470 3.84 - 4.37: 14315 4.37 - 4.90: 24966 Nonbonded interactions: 59919 Sorted by model distance: nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASN R 86 " pdb=" OG1 THR R 135 " model vdw 2.253 3.040 nonbonded pdb=" NH2 ARG H 70 " pdb=" OD2 ASP H 93 " model vdw 2.274 3.120 nonbonded pdb=" OE2 GLU K 6 " pdb=" N GLY K 114 " model vdw 2.275 3.120 nonbonded pdb=" O TYR L 50 " pdb=" OG SER L 54 " model vdw 2.282 3.040 ... (remaining 59914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7445 Z= 0.120 Angle : 0.506 7.882 10134 Z= 0.264 Chirality : 0.041 0.146 1156 Planarity : 0.003 0.046 1275 Dihedral : 14.666 89.805 2607 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.13 % Allowed : 17.59 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.72 (0.28), residues: 936 helix: 1.78 (0.28), residues: 342 sheet: -0.40 (0.30), residues: 278 loop : 0.04 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 248 TYR 0.014 0.001 TYR L 92 PHE 0.012 0.001 PHE R 83 TRP 0.011 0.001 TRP H 117 HIS 0.001 0.000 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7439) covalent geometry : angle 0.50510 (10122) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.98965 ( 12) hydrogen bonds : bond 0.14324 ( 432) hydrogen bonds : angle 6.61841 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 267 ILE cc_start: 0.7473 (mt) cc_final: 0.5780 (tp) REVERT: H 189 LEU cc_start: 0.8783 (mm) cc_final: 0.8433 (mt) REVERT: L 171 LYS cc_start: 0.8124 (mptt) cc_final: 0.7860 (mmtt) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.4686 time to fit residues: 87.0272 Evaluate side-chains 114 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 GLN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 183 HIS R 338 GLN ** R 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 ASN R 422 ASN R 426 ASN R 436 ASN H 31 ASN H 85 GLN H 185 GLN H 211 ASN H 213 ASN H 214 HIS K 77 ASN L 149 GLN L 154 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.212835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.169587 restraints weight = 7371.679| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.48 r_work: 0.3449 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7445 Z= 0.170 Angle : 0.596 6.606 10134 Z= 0.311 Chirality : 0.043 0.161 1156 Planarity : 0.004 0.042 1275 Dihedral : 4.197 17.737 1022 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.92 % Allowed : 20.31 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.94 (0.28), residues: 936 helix: 2.04 (0.27), residues: 346 sheet: -0.26 (0.30), residues: 275 loop : 0.01 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 358 TYR 0.016 0.002 TYR R 396 PHE 0.018 0.002 PHE K 47 TRP 0.012 0.001 TRP R 384 HIS 0.001 0.000 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7439) covalent geometry : angle 0.59486 (10122) SS BOND : bond 0.00152 ( 6) SS BOND : angle 1.25089 ( 12) hydrogen bonds : bond 0.04122 ( 432) hydrogen bonds : angle 5.02434 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 MET cc_start: 0.4599 (ttm) cc_final: 0.4320 (tmm) REVERT: R 120 ILE cc_start: 0.7589 (tt) cc_final: 0.7314 (tp) REVERT: R 247 ARG cc_start: 0.7134 (ttp-110) cc_final: 0.6718 (mtm-85) REVERT: R 354 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6144 (pttt) REVERT: R 420 PHE cc_start: 0.6146 (m-10) cc_final: 0.5899 (m-80) REVERT: R 428 ILE cc_start: 0.7448 (tt) cc_final: 0.7059 (tp) REVERT: K 99 ASP cc_start: 0.7561 (p0) cc_final: 0.7337 (p0) REVERT: L 147 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8156 (pptt) REVERT: L 171 LYS cc_start: 0.8332 (mptt) cc_final: 0.8064 (mmtt) REVERT: L 185 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7322 (ttmt) outliers start: 38 outliers final: 9 residues processed: 142 average time/residue: 0.5194 time to fit residues: 78.2670 Evaluate side-chains 116 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 354 LYS Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 185 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 338 GLN R 367 GLN R 408 ASN R 436 ASN H 211 ASN K 65 GLN L 149 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.207145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153848 restraints weight = 7299.542| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.55 r_work: 0.3349 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7445 Z= 0.200 Angle : 0.615 7.848 10134 Z= 0.317 Chirality : 0.044 0.155 1156 Planarity : 0.004 0.038 1275 Dihedral : 4.379 18.635 1020 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.43 % Allowed : 21.22 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.95 (0.28), residues: 936 helix: 2.16 (0.27), residues: 347 sheet: -0.32 (0.30), residues: 282 loop : -0.06 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 72 TYR 0.015 0.002 TYR H 159 PHE 0.021 0.002 PHE K 47 TRP 0.013 0.001 TRP R 384 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 7439) covalent geometry : angle 0.61311 (10122) SS BOND : bond 0.00232 ( 6) SS BOND : angle 1.37413 ( 12) hydrogen bonds : bond 0.03839 ( 432) hydrogen bonds : angle 5.00708 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 232 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5642 (pp) REVERT: R 247 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6784 (mtm-85) REVERT: R 336 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6517 (pm20) REVERT: R 351 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: R 408 ASN cc_start: 0.6431 (m-40) cc_final: 0.6228 (m110) REVERT: R 433 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6338 (t80) REVERT: L 82 GLU cc_start: 0.8288 (pm20) cc_final: 0.8071 (pm20) REVERT: L 135 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8638 (t) REVERT: L 171 LYS cc_start: 0.8451 (mptt) cc_final: 0.8169 (mmtt) outliers start: 42 outliers final: 19 residues processed: 147 average time/residue: 0.5255 time to fit residues: 81.9872 Evaluate side-chains 135 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 336 GLU Chi-restraints excluded: chain R residue 346 THR Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 433 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 147 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 436 ASN K 84 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.209693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.163018 restraints weight = 7410.452| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.41 r_work: 0.3398 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7445 Z= 0.148 Angle : 0.578 9.588 10134 Z= 0.297 Chirality : 0.042 0.154 1156 Planarity : 0.004 0.038 1275 Dihedral : 4.156 18.459 1020 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.27 % Allowed : 23.29 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.06 (0.28), residues: 936 helix: 2.28 (0.27), residues: 347 sheet: -0.28 (0.30), residues: 277 loop : -0.04 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.014 0.001 TYR L 142 PHE 0.015 0.001 PHE K 47 TRP 0.011 0.001 TRP H 117 HIS 0.001 0.000 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7439) covalent geometry : angle 0.57718 (10122) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.97980 ( 12) hydrogen bonds : bond 0.03431 ( 432) hydrogen bonds : angle 4.83327 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 60 MET cc_start: 0.5967 (mmm) cc_final: 0.5737 (mmt) REVERT: R 232 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5611 (pp) REVERT: R 247 ARG cc_start: 0.7305 (ttp-110) cc_final: 0.6980 (mtm-85) REVERT: R 268 GLU cc_start: 0.6669 (mp0) cc_final: 0.6342 (mp0) REVERT: R 416 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6562 (t-90) REVERT: H 92 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: K 38 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6879 (ttm170) REVERT: L 135 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8650 (t) REVERT: L 171 LYS cc_start: 0.8487 (mptt) cc_final: 0.8217 (mmtt) outliers start: 33 outliers final: 15 residues processed: 137 average time/residue: 0.5329 time to fit residues: 77.4798 Evaluate side-chains 123 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 424 SER Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 147 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 93 optimal weight: 0.0170 chunk 26 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 338 GLN R 408 ASN R 436 ASN ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.210929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164821 restraints weight = 7282.740| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.38 r_work: 0.3436 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7445 Z= 0.127 Angle : 0.558 8.812 10134 Z= 0.284 Chirality : 0.041 0.181 1156 Planarity : 0.003 0.035 1275 Dihedral : 4.026 18.030 1020 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.27 % Allowed : 23.29 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.30 (0.29), residues: 936 helix: 2.46 (0.28), residues: 347 sheet: -0.11 (0.31), residues: 275 loop : 0.06 (0.39), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 143 TYR 0.012 0.001 TYR L 142 PHE 0.012 0.001 PHE K 47 TRP 0.010 0.001 TRP H 117 HIS 0.001 0.000 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7439) covalent geometry : angle 0.55791 (10122) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.88234 ( 12) hydrogen bonds : bond 0.03266 ( 432) hydrogen bonds : angle 4.69227 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 232 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5642 (pp) REVERT: R 238 MET cc_start: 0.6704 (ttm) cc_final: 0.6488 (ptp) REVERT: R 247 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6966 (mtm-85) REVERT: R 268 GLU cc_start: 0.6674 (mp0) cc_final: 0.6357 (mp0) REVERT: R 416 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.6496 (t-90) REVERT: R 433 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6383 (t80) REVERT: H 189 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8341 (mt) REVERT: H 197 THR cc_start: 0.8770 (m) cc_final: 0.8367 (p) REVERT: K 38 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6952 (ttm170) REVERT: L 135 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8629 (t) REVERT: L 171 LYS cc_start: 0.8485 (mptt) cc_final: 0.8228 (mmtt) outliers start: 33 outliers final: 17 residues processed: 142 average time/residue: 0.4992 time to fit residues: 75.6183 Evaluate side-chains 126 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 424 SER Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 433 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 147 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 0.0060 chunk 73 optimal weight: 0.0170 chunk 86 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN R 408 ASN H 211 ASN K 84 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.209654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.157761 restraints weight = 7393.462| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.54 r_work: 0.3404 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7445 Z= 0.123 Angle : 0.552 8.542 10134 Z= 0.278 Chirality : 0.041 0.192 1156 Planarity : 0.004 0.054 1275 Dihedral : 3.961 17.885 1020 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.79 % Allowed : 23.16 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.40 (0.29), residues: 936 helix: 2.53 (0.28), residues: 347 sheet: -0.04 (0.31), residues: 275 loop : 0.12 (0.39), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 358 TYR 0.012 0.001 TYR L 142 PHE 0.012 0.001 PHE K 47 TRP 0.010 0.001 TRP H 117 HIS 0.001 0.000 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7439) covalent geometry : angle 0.55188 (10122) SS BOND : bond 0.00217 ( 6) SS BOND : angle 0.84702 ( 12) hydrogen bonds : bond 0.03217 ( 432) hydrogen bonds : angle 4.61929 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 232 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5693 (pp) REVERT: R 238 MET cc_start: 0.6690 (ttm) cc_final: 0.6468 (ptp) REVERT: R 247 ARG cc_start: 0.7294 (ttp-110) cc_final: 0.7001 (mtm-85) REVERT: R 278 ASP cc_start: 0.6923 (m-30) cc_final: 0.6666 (m-30) REVERT: R 381 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6405 (mp) REVERT: R 408 ASN cc_start: 0.6380 (m-40) cc_final: 0.6139 (m110) REVERT: R 416 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.6575 (t-90) REVERT: R 433 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6348 (t80) REVERT: H 92 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: H 189 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8322 (mt) REVERT: H 197 THR cc_start: 0.8784 (m) cc_final: 0.8402 (p) REVERT: K 38 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6899 (ttm170) REVERT: L 135 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8593 (t) REVERT: L 171 LYS cc_start: 0.8471 (mptt) cc_final: 0.8209 (mmtt) outliers start: 37 outliers final: 18 residues processed: 142 average time/residue: 0.4914 time to fit residues: 74.5045 Evaluate side-chains 132 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 424 SER Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 433 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 147 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN K 84 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.207427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.155172 restraints weight = 7272.834| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.52 r_work: 0.3370 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7445 Z= 0.161 Angle : 0.629 16.898 10134 Z= 0.307 Chirality : 0.043 0.212 1156 Planarity : 0.004 0.050 1275 Dihedral : 4.119 18.634 1020 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.66 % Allowed : 24.06 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.30 (0.29), residues: 936 helix: 2.48 (0.28), residues: 346 sheet: -0.13 (0.31), residues: 281 loop : 0.09 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 143 TYR 0.013 0.001 TYR L 142 PHE 0.016 0.001 PHE K 47 TRP 0.011 0.001 TRP H 117 HIS 0.001 0.000 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7439) covalent geometry : angle 0.62786 (10122) SS BOND : bond 0.00213 ( 6) SS BOND : angle 1.04413 ( 12) hydrogen bonds : bond 0.03425 ( 432) hydrogen bonds : angle 4.71312 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 60 MET cc_start: 0.6435 (mmm) cc_final: 0.6006 (ptm) REVERT: R 232 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5634 (pp) REVERT: R 247 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7074 (mtm-85) REVERT: R 381 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6407 (mp) REVERT: R 433 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6380 (t80) REVERT: H 92 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: H 189 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8362 (mt) REVERT: H 197 THR cc_start: 0.8845 (m) cc_final: 0.8399 (p) REVERT: K 38 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6551 (ttm170) REVERT: L 135 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8609 (t) REVERT: L 171 LYS cc_start: 0.8421 (mptt) cc_final: 0.8153 (mmtt) outliers start: 36 outliers final: 20 residues processed: 139 average time/residue: 0.4941 time to fit residues: 73.1476 Evaluate side-chains 131 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 346 THR Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 424 SER Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 433 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.204198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149162 restraints weight = 7388.493| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.66 r_work: 0.3210 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 7445 Z= 0.243 Angle : 0.687 14.117 10134 Z= 0.342 Chirality : 0.046 0.243 1156 Planarity : 0.004 0.052 1275 Dihedral : 4.466 19.819 1020 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.43 % Allowed : 23.93 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.04 (0.29), residues: 936 helix: 2.26 (0.28), residues: 346 sheet: -0.28 (0.30), residues: 287 loop : -0.04 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 72 TYR 0.017 0.002 TYR L 142 PHE 0.023 0.002 PHE K 47 TRP 0.011 0.002 TRP H 117 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 7439) covalent geometry : angle 0.68616 (10122) SS BOND : bond 0.00352 ( 6) SS BOND : angle 1.34757 ( 12) hydrogen bonds : bond 0.03855 ( 432) hydrogen bonds : angle 4.99952 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 143 ARG cc_start: 0.5880 (mtt180) cc_final: 0.5533 (mtt-85) REVERT: R 232 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5577 (pp) REVERT: R 247 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6964 (mtm-85) REVERT: R 351 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: R 381 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6284 (mp) REVERT: H 92 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: H 189 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8317 (mp) REVERT: K 38 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6655 (ttm170) REVERT: L 135 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8623 (t) REVERT: L 171 LYS cc_start: 0.8472 (mptt) cc_final: 0.8124 (mmtt) outliers start: 42 outliers final: 24 residues processed: 142 average time/residue: 0.5053 time to fit residues: 76.4447 Evaluate side-chains 134 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 336 GLU Chi-restraints excluded: chain R residue 346 THR Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 424 SER Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.207172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.154537 restraints weight = 7328.668| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.57 r_work: 0.3366 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7445 Z= 0.141 Angle : 0.626 11.515 10134 Z= 0.310 Chirality : 0.042 0.231 1156 Planarity : 0.004 0.046 1275 Dihedral : 4.201 18.677 1020 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.88 % Allowed : 25.61 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.13 (0.29), residues: 936 helix: 2.23 (0.28), residues: 346 sheet: -0.15 (0.31), residues: 281 loop : 0.05 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 19 TYR 0.014 0.001 TYR L 142 PHE 0.013 0.001 PHE R 48 TRP 0.011 0.001 TRP H 117 HIS 0.002 0.001 HIS R 77 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7439) covalent geometry : angle 0.61620 (10122) SS BOND : bond 0.00265 ( 6) SS BOND : angle 3.25322 ( 12) hydrogen bonds : bond 0.03434 ( 432) hydrogen bonds : angle 4.77513 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 60 MET cc_start: 0.6117 (mmm) cc_final: 0.5698 (ttt) REVERT: R 61 MET cc_start: 0.6310 (ttp) cc_final: 0.5496 (tmm) REVERT: R 143 ARG cc_start: 0.6020 (mtt180) cc_final: 0.5711 (mtt-85) REVERT: R 232 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5638 (pp) REVERT: R 244 ILE cc_start: 0.7673 (mm) cc_final: 0.7197 (tp) REVERT: R 247 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.7116 (mtm-85) REVERT: R 278 ASP cc_start: 0.6948 (m-30) cc_final: 0.6698 (m-30) REVERT: H 92 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: H 189 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8369 (mt) REVERT: K 38 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6346 (ttm170) REVERT: L 135 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8606 (t) REVERT: L 171 LYS cc_start: 0.8414 (mptt) cc_final: 0.8160 (mmtt) outliers start: 30 outliers final: 22 residues processed: 133 average time/residue: 0.5086 time to fit residues: 71.9403 Evaluate side-chains 131 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 336 GLU Chi-restraints excluded: chain R residue 346 THR Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 424 SER Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 147 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.0000 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.204447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.150939 restraints weight = 7347.683| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.52 r_work: 0.3238 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7445 Z= 0.198 Angle : 0.670 10.783 10134 Z= 0.333 Chirality : 0.044 0.244 1156 Planarity : 0.004 0.048 1275 Dihedral : 4.389 19.476 1020 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.01 % Allowed : 26.39 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.04 (0.29), residues: 936 helix: 2.22 (0.28), residues: 346 sheet: -0.26 (0.30), residues: 282 loop : -0.00 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.020 0.002 TYR R 355 PHE 0.019 0.002 PHE K 47 TRP 0.013 0.001 TRP H 117 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 7439) covalent geometry : angle 0.66250 (10122) SS BOND : bond 0.00320 ( 6) SS BOND : angle 2.90997 ( 12) hydrogen bonds : bond 0.03683 ( 432) hydrogen bonds : angle 4.93232 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 60 MET cc_start: 0.6129 (mmm) cc_final: 0.5658 (ttt) REVERT: R 61 MET cc_start: 0.6384 (ttp) cc_final: 0.5542 (tmm) REVERT: R 143 ARG cc_start: 0.5805 (mtt180) cc_final: 0.5474 (mtt-85) REVERT: R 232 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5523 (pp) REVERT: R 247 ARG cc_start: 0.7204 (ttp-110) cc_final: 0.6948 (mtm-85) REVERT: R 278 ASP cc_start: 0.7109 (m-30) cc_final: 0.6862 (m-30) REVERT: R 381 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6246 (mp) REVERT: R 391 MET cc_start: 0.6230 (mtm) cc_final: 0.5849 (mmt) REVERT: H 92 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: H 189 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8332 (mt) REVERT: K 38 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6576 (ttm170) REVERT: L 135 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8582 (t) REVERT: L 171 LYS cc_start: 0.8484 (mptt) cc_final: 0.8163 (mmtt) outliers start: 31 outliers final: 23 residues processed: 127 average time/residue: 0.5098 time to fit residues: 68.9955 Evaluate side-chains 129 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 336 GLU Chi-restraints excluded: chain R residue 346 THR Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 424 SER Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.203776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150159 restraints weight = 7341.445| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.54 r_work: 0.3328 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7445 Z= 0.201 Angle : 0.665 10.323 10134 Z= 0.331 Chirality : 0.044 0.239 1156 Planarity : 0.004 0.049 1275 Dihedral : 4.424 20.148 1020 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.14 % Allowed : 26.13 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.02 (0.29), residues: 936 helix: 2.17 (0.28), residues: 350 sheet: -0.30 (0.30), residues: 282 loop : 0.03 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 72 TYR 0.020 0.002 TYR R 355 PHE 0.020 0.002 PHE R 48 TRP 0.013 0.001 TRP H 117 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7439) covalent geometry : angle 0.65891 (10122) SS BOND : bond 0.00351 ( 6) SS BOND : angle 2.69421 ( 12) hydrogen bonds : bond 0.03674 ( 432) hydrogen bonds : angle 4.96799 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3416.47 seconds wall clock time: 58 minutes 59.97 seconds (3539.97 seconds total)