Starting phenix.real_space_refine on Mon Apr 28 08:52:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jg0_61446/04_2025/9jg0_61446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jg0_61446/04_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_61446/04_2025/9jg0_61446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jg0_61446/04_2025/9jg0_61446.map" model { file = "/net/cci-nas-00/data/ceres_data/9jg0_61446/04_2025/9jg0_61446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jg0_61446/04_2025/9jg0_61446.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5} 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: 5.00, per 1000 atoms: 0.69 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.15 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: 3.32 Time building geometry restraints manager: 2.18 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: 1.900 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.100 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.980 ------------------------------------------------------------------------------- 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 : 8.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (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 TRP 0.011 0.001 TRP H 117 HIS 0.001 0.000 HIS L 200 PHE 0.012 0.001 PHE R 83 TYR 0.014 0.001 TYR L 92 ARG 0.003 0.000 ARG R 248 Details of bonding type rmsd hydrogen bonds : bond 0.14324 ( 432) hydrogen bonds : angle 6.61841 ( 1278) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.98965 ( 12) covalent geometry : bond 0.00268 ( 7439) covalent geometry : angle 0.50510 (10122) *********************** 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 : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 267 ILE cc_start: 0.7473 (mt) cc_final: 0.5781 (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: 1.0896 time to fit residues: 202.3588 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 : 1.119 ------------------------------------------------------------------------------- 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 79 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.0170 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 261 ASN R 338 GLN R 367 GLN 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 154 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.210982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.166016 restraints weight = 7283.616| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.44 r_work: 0.3406 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2801 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 : 0.626 7.724 10134 Z= 0.326 Chirality : 0.045 0.160 1156 Planarity : 0.004 0.043 1275 Dihedral : 4.353 18.133 1022 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.95 % Allowed : 19.92 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.28), residues: 936 helix: 2.00 (0.27), residues: 344 sheet: -0.30 (0.31), residues: 275 loop : -0.03 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 384 HIS 0.002 0.001 HIS H 38 PHE 0.021 0.002 PHE K 47 TYR 0.017 0.002 TYR H 159 ARG 0.003 0.001 ARG K 72 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 432) hydrogen bonds : angle 5.10593 ( 1278) SS BOND : bond 0.00517 ( 6) SS BOND : angle 1.29176 ( 12) covalent geometry : bond 0.00470 ( 7439) covalent geometry : angle 0.62526 (10122) *********************** 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 166 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 MET cc_start: 0.4706 (ttm) cc_final: 0.4394 (tmm) REVERT: R 247 ARG cc_start: 0.7158 (ttp-110) cc_final: 0.6747 (mtm-85) REVERT: R 268 GLU cc_start: 0.7006 (tp30) cc_final: 0.6741 (mm-30) REVERT: R 342 GLU cc_start: 0.7611 (tp30) cc_final: 0.7375 (tp30) REVERT: R 354 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6119 (pttt) REVERT: H 189 LEU cc_start: 0.8809 (mm) cc_final: 0.8373 (mt) REVERT: K 99 ASP cc_start: 0.7573 (p0) cc_final: 0.7369 (p0) REVERT: L 171 LYS cc_start: 0.8379 (mptt) cc_final: 0.8108 (mmtt) REVERT: L 185 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7312 (ttmt) outliers start: 46 outliers final: 15 residues processed: 149 average time/residue: 1.3349 time to fit residues: 211.9604 Evaluate side-chains 122 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 15 VAL Chi-restraints excluded: chain H residue 33 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 34 MET Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 73 THR 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 18 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 H 211 ASN K 65 GLN ** 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 = 0.4221 r_free = 0.4221 target = 0.208710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154489 restraints weight = 7396.537| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.54 r_work: 0.3367 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.004 0.052 7445 Z= 0.159 Angle : 0.576 6.530 10134 Z= 0.297 Chirality : 0.043 0.158 1156 Planarity : 0.004 0.039 1275 Dihedral : 4.233 18.312 1020 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.92 % Allowed : 21.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 936 helix: 2.20 (0.27), residues: 347 sheet: -0.28 (0.30), residues: 277 loop : -0.03 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 117 HIS 0.002 0.001 HIS H 214 PHE 0.017 0.001 PHE K 47 TYR 0.013 0.001 TYR L 142 ARG 0.002 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 432) hydrogen bonds : angle 4.89546 ( 1278) SS BOND : bond 0.00225 ( 6) SS BOND : angle 1.17749 ( 12) covalent geometry : bond 0.00371 ( 7439) covalent geometry : angle 0.57445 (10122) *********************** 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 153 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 60 MET cc_start: 0.6754 (mmm) cc_final: 0.6545 (mmm) REVERT: R 99 MET cc_start: 0.4895 (ttm) cc_final: 0.4420 (tmm) REVERT: R 232 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5596 (pp) REVERT: R 247 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6832 (mtm-85) REVERT: R 268 GLU cc_start: 0.7055 (tp30) cc_final: 0.6770 (mm-30) REVERT: R 342 GLU cc_start: 0.7711 (tp30) cc_final: 0.7445 (tp30) REVERT: R 416 HIS cc_start: 0.6883 (OUTLIER) cc_final: 0.6627 (t-90) REVERT: R 433 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6496 (t80) REVERT: H 165 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7961 (m) REVERT: H 197 THR cc_start: 0.8795 (m) cc_final: 0.8372 (p) REVERT: L 71 ASP cc_start: 0.8414 (m-30) cc_final: 0.7945 (m-30) REVERT: L 97 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8088 (mt) REVERT: L 135 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8642 (t) REVERT: L 171 LYS cc_start: 0.8428 (mptt) cc_final: 0.8160 (mmtt) outliers start: 38 outliers final: 15 residues processed: 142 average time/residue: 1.5979 time to fit residues: 241.6830 Evaluate side-chains 129 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 346 THR Chi-restraints excluded: chain R residue 416 HIS 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 60 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 20 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 7 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 408 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 = 0.4200 r_free = 0.4200 target = 0.206186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.152852 restraints weight = 7414.245| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.54 r_work: 0.3353 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7445 Z= 0.190 Angle : 0.614 9.460 10134 Z= 0.315 Chirality : 0.044 0.174 1156 Planarity : 0.004 0.038 1275 Dihedral : 4.333 19.206 1020 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.92 % Allowed : 22.90 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.28), residues: 936 helix: 2.24 (0.27), residues: 348 sheet: -0.29 (0.30), residues: 276 loop : -0.06 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 117 HIS 0.003 0.001 HIS L 200 PHE 0.019 0.002 PHE K 47 TYR 0.015 0.002 TYR H 159 ARG 0.003 0.000 ARG K 72 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 432) hydrogen bonds : angle 4.92847 ( 1278) SS BOND : bond 0.00185 ( 6) SS BOND : angle 1.22381 ( 12) covalent geometry : bond 0.00444 ( 7439) covalent geometry : angle 0.61302 (10122) *********************** 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 148 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 60 MET cc_start: 0.6848 (mmm) cc_final: 0.6437 (mmt) REVERT: R 232 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5555 (pp) REVERT: R 247 ARG cc_start: 0.7300 (ttp-110) cc_final: 0.7056 (mtm-85) REVERT: R 268 GLU cc_start: 0.6921 (tp30) cc_final: 0.6526 (mm-30) REVERT: R 342 GLU cc_start: 0.7824 (tp30) cc_final: 0.7461 (tp30) REVERT: R 381 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6475 (mp) REVERT: R 408 ASN cc_start: 0.6491 (m-40) cc_final: 0.6243 (m110) REVERT: R 416 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.6652 (t-90) REVERT: K 38 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7361 (ttm170) REVERT: K 99 ASP cc_start: 0.7683 (p0) cc_final: 0.7444 (p0) REVERT: L 71 ASP cc_start: 0.8385 (m-30) cc_final: 0.7840 (m-30) REVERT: L 135 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8603 (t) REVERT: L 171 LYS cc_start: 0.8431 (mptt) cc_final: 0.8168 (mmtt) outliers start: 38 outliers final: 23 residues processed: 140 average time/residue: 0.9715 time to fit residues: 146.2068 Evaluate side-chains 129 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 346 THR Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 425 VAL 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 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 102 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 K 84 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.209370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165642 restraints weight = 7319.107| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.47 r_work: 0.3405 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3878 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= 0.142 Angle : 0.583 12.472 10134 Z= 0.293 Chirality : 0.042 0.185 1156 Planarity : 0.004 0.037 1275 Dihedral : 4.134 18.867 1020 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.53 % Allowed : 24.06 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 936 helix: 2.37 (0.27), residues: 348 sheet: -0.22 (0.30), residues: 282 loop : 0.04 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 117 HIS 0.001 0.000 HIS H 214 PHE 0.014 0.001 PHE K 47 TYR 0.014 0.001 TYR L 142 ARG 0.002 0.000 ARG R 358 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 432) hydrogen bonds : angle 4.72893 ( 1278) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.90096 ( 12) covalent geometry : bond 0.00329 ( 7439) covalent geometry : angle 0.58224 (10122) *********************** 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 147 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 232 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5591 (pp) REVERT: R 247 ARG cc_start: 0.7382 (ttp-110) cc_final: 0.7079 (mtm-85) REVERT: R 261 ASN cc_start: 0.8143 (m110) cc_final: 0.7746 (m110) REVERT: R 342 GLU cc_start: 0.7901 (tp30) cc_final: 0.7689 (tp30) REVERT: R 408 ASN cc_start: 0.6381 (m-40) cc_final: 0.6147 (m110) REVERT: R 416 HIS cc_start: 0.6822 (OUTLIER) cc_final: 0.6612 (t-90) REVERT: R 433 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6548 (t80) REVERT: H 197 THR cc_start: 0.8798 (m) cc_final: 0.8389 (p) REVERT: L 71 ASP cc_start: 0.8405 (m-30) cc_final: 0.7877 (m-30) REVERT: L 135 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8635 (t) REVERT: L 171 LYS cc_start: 0.8446 (mptt) cc_final: 0.8221 (mmtt) outliers start: 35 outliers final: 20 residues processed: 139 average time/residue: 0.9017 time to fit residues: 134.3815 Evaluate side-chains 127 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 336 GLU Chi-restraints excluded: chain R residue 416 HIS 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 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 86 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain K residue 83 MET 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 23 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 50 optimal weight: 0.1980 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 H 211 ASN K 84 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.209669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.162558 restraints weight = 7280.444| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.39 r_work: 0.3424 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7445 Z= 0.127 Angle : 0.576 8.492 10134 Z= 0.288 Chirality : 0.042 0.216 1156 Planarity : 0.003 0.037 1275 Dihedral : 4.034 18.136 1020 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.66 % Allowed : 23.54 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 936 helix: 2.51 (0.28), residues: 347 sheet: -0.08 (0.31), residues: 280 loop : 0.14 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 117 HIS 0.001 0.000 HIS H 214 PHE 0.013 0.001 PHE K 47 TYR 0.013 0.001 TYR R 410 ARG 0.003 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 432) hydrogen bonds : angle 4.62421 ( 1278) SS BOND : bond 0.00222 ( 6) SS BOND : angle 0.86331 ( 12) covalent geometry : bond 0.00291 ( 7439) covalent geometry : angle 0.57542 (10122) *********************** 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 154 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 PHE cc_start: 0.6724 (m-80) cc_final: 0.6070 (m-10) REVERT: R 232 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5588 (pp) REVERT: R 247 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.7026 (mtm-85) REVERT: R 268 GLU cc_start: 0.6643 (mp0) cc_final: 0.6299 (mp0) REVERT: R 278 ASP cc_start: 0.6876 (m-30) cc_final: 0.6627 (m-30) REVERT: R 342 GLU cc_start: 0.7707 (tp30) cc_final: 0.7462 (tp30) REVERT: R 416 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6576 (t-90) REVERT: R 433 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6407 (t80) REVERT: H 197 THR cc_start: 0.8801 (m) cc_final: 0.8418 (p) REVERT: L 71 ASP cc_start: 0.8391 (m-30) cc_final: 0.7850 (m-30) REVERT: L 135 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8615 (t) REVERT: L 171 LYS cc_start: 0.8425 (mptt) cc_final: 0.8210 (mmtt) outliers start: 36 outliers final: 20 residues processed: 144 average time/residue: 1.4122 time to fit residues: 214.2114 Evaluate side-chains 131 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 336 GLU Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 416 HIS 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 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 165 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 83 MET 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 65 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.207228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.155184 restraints weight = 7293.010| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.44 r_work: 0.3383 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4203 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= 0.156 Angle : 0.605 9.866 10134 Z= 0.305 Chirality : 0.043 0.232 1156 Planarity : 0.004 0.037 1275 Dihedral : 4.188 18.987 1020 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 5.17 % Allowed : 24.06 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 936 helix: 2.40 (0.28), residues: 347 sheet: -0.11 (0.31), residues: 281 loop : 0.10 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 117 HIS 0.001 0.001 HIS H 214 PHE 0.016 0.001 PHE K 47 TYR 0.014 0.001 TYR L 142 ARG 0.004 0.000 ARG R 143 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 432) hydrogen bonds : angle 4.72739 ( 1278) SS BOND : bond 0.00237 ( 6) SS BOND : angle 1.00282 ( 12) covalent geometry : bond 0.00360 ( 7439) covalent geometry : angle 0.60467 (10122) *********************** 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 142 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 PHE cc_start: 0.6763 (m-80) cc_final: 0.6075 (m-10) REVERT: R 175 MET cc_start: 0.4620 (pmm) cc_final: 0.3767 (ptp) REVERT: R 232 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5705 (pp) REVERT: R 244 ILE cc_start: 0.7600 (mm) cc_final: 0.7122 (tp) REVERT: R 247 ARG cc_start: 0.7347 (ttp-110) cc_final: 0.7094 (mtm-85) REVERT: R 268 GLU cc_start: 0.6719 (mp0) cc_final: 0.6458 (mm-30) REVERT: R 342 GLU cc_start: 0.7689 (tp30) cc_final: 0.7358 (tp30) REVERT: R 381 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6483 (mp) REVERT: R 433 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6352 (t80) REVERT: H 197 THR cc_start: 0.8834 (m) cc_final: 0.8420 (p) REVERT: L 71 ASP cc_start: 0.8389 (m-30) cc_final: 0.7840 (m-30) REVERT: L 135 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8611 (t) REVERT: L 171 LYS cc_start: 0.8432 (mptt) cc_final: 0.8186 (mmtt) outliers start: 40 outliers final: 26 residues processed: 133 average time/residue: 1.6564 time to fit residues: 230.6616 Evaluate side-chains 129 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 390 LEU 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 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 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 165 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain H residue 221 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.205742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151765 restraints weight = 7397.277| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.50 r_work: 0.3265 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7445 Z= 0.178 Angle : 0.625 9.433 10134 Z= 0.314 Chirality : 0.043 0.229 1156 Planarity : 0.004 0.036 1275 Dihedral : 4.265 19.444 1020 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.92 % Allowed : 24.97 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 936 helix: 2.27 (0.28), residues: 347 sheet: -0.17 (0.31), residues: 282 loop : 0.06 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 117 HIS 0.002 0.001 HIS L 200 PHE 0.018 0.002 PHE K 47 TYR 0.014 0.001 TYR L 142 ARG 0.005 0.000 ARG R 143 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 432) hydrogen bonds : angle 4.81530 ( 1278) SS BOND : bond 0.00235 ( 6) SS BOND : angle 1.08019 ( 12) covalent geometry : bond 0.00416 ( 7439) covalent geometry : angle 0.62447 (10122) *********************** 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 141 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 60 MET cc_start: 0.6633 (tpp) cc_final: 0.5717 (tmm) REVERT: R 120 ILE cc_start: 0.7288 (tt) cc_final: 0.7087 (tp) REVERT: R 143 ARG cc_start: 0.5831 (mmt180) cc_final: 0.5486 (mtt180) REVERT: R 175 MET cc_start: 0.5020 (pmm) cc_final: 0.4184 (ptp) REVERT: R 181 MET cc_start: 0.4027 (ppp) cc_final: 0.3767 (pp-130) REVERT: R 232 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5521 (pp) REVERT: R 244 ILE cc_start: 0.7540 (mm) cc_final: 0.7083 (tp) REVERT: R 247 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6953 (mtm-85) REVERT: R 268 GLU cc_start: 0.6768 (mp0) cc_final: 0.6486 (mm-30) REVERT: R 292 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6575 (mtpp) REVERT: R 342 GLU cc_start: 0.7728 (tp30) cc_final: 0.7273 (tp30) REVERT: R 381 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6240 (mp) REVERT: R 391 MET cc_start: 0.6259 (mtm) cc_final: 0.5942 (mtt) REVERT: L 71 ASP cc_start: 0.8409 (m-30) cc_final: 0.7836 (m-30) REVERT: L 135 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8599 (t) REVERT: L 171 LYS cc_start: 0.8460 (mptt) cc_final: 0.8144 (mmtt) outliers start: 38 outliers final: 26 residues processed: 132 average time/residue: 3.4042 time to fit residues: 464.2928 Evaluate side-chains 130 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 292 LYS 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 390 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain H residue 5 VAL 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 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 165 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 221 VAL 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 Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.0770 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.205780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153266 restraints weight = 7425.500| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.52 r_work: 0.3361 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4460 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= 0.153 Angle : 0.612 9.773 10134 Z= 0.308 Chirality : 0.043 0.231 1156 Planarity : 0.004 0.036 1275 Dihedral : 4.178 18.816 1020 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.40 % Allowed : 25.49 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 936 helix: 2.26 (0.28), residues: 347 sheet: -0.12 (0.31), residues: 281 loop : 0.14 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 117 HIS 0.001 0.000 HIS H 214 PHE 0.015 0.001 PHE K 47 TYR 0.014 0.001 TYR L 142 ARG 0.004 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 432) hydrogen bonds : angle 4.74670 ( 1278) SS BOND : bond 0.00283 ( 6) SS BOND : angle 2.82638 ( 12) covalent geometry : bond 0.00355 ( 7439) covalent geometry : angle 0.60429 (10122) *********************** 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 134 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 175 MET cc_start: 0.4949 (pmm) cc_final: 0.3920 (ptp) REVERT: R 181 MET cc_start: 0.3904 (ppp) cc_final: 0.3600 (pp-130) REVERT: R 232 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5624 (pp) REVERT: R 244 ILE cc_start: 0.7650 (mm) cc_final: 0.7167 (tp) REVERT: R 247 ARG cc_start: 0.7382 (ttp-110) cc_final: 0.7091 (mtm-85) REVERT: R 268 GLU cc_start: 0.6818 (mp0) cc_final: 0.6542 (mm-30) REVERT: R 292 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6588 (mtpp) REVERT: R 342 GLU cc_start: 0.7798 (tp30) cc_final: 0.7356 (tp30) REVERT: R 381 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6457 (mp) REVERT: R 391 MET cc_start: 0.6344 (mtm) cc_final: 0.6003 (mtt) REVERT: H 197 THR cc_start: 0.8843 (m) cc_final: 0.8412 (p) REVERT: L 71 ASP cc_start: 0.8476 (m-30) cc_final: 0.7941 (m-30) REVERT: L 135 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8595 (t) REVERT: L 171 LYS cc_start: 0.8413 (mptt) cc_final: 0.8168 (mmtt) outliers start: 34 outliers final: 27 residues processed: 129 average time/residue: 0.9289 time to fit residues: 128.3578 Evaluate side-chains 127 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 245 SER Chi-restraints excluded: chain R residue 292 LYS 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 390 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain H residue 5 VAL 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 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 165 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain K residue 83 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 102 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 = 0.4196 r_free = 0.4196 target = 0.205685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.152643 restraints weight = 7449.328| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.54 r_work: 0.3260 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4523 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= 0.156 Angle : 0.624 12.251 10134 Z= 0.312 Chirality : 0.043 0.236 1156 Planarity : 0.004 0.036 1275 Dihedral : 4.251 18.947 1020 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.40 % Allowed : 25.61 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 936 helix: 2.24 (0.28), residues: 347 sheet: -0.12 (0.31), residues: 281 loop : 0.14 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 117 HIS 0.002 0.001 HIS R 313 PHE 0.033 0.002 PHE R 311 TYR 0.017 0.001 TYR R 430 ARG 0.006 0.000 ARG R 143 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 432) hydrogen bonds : angle 4.77947 ( 1278) SS BOND : bond 0.00275 ( 6) SS BOND : angle 2.28293 ( 12) covalent geometry : bond 0.00363 ( 7439) covalent geometry : angle 0.61963 (10122) ********************** 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 132 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 MET cc_start: 0.6514 (ttp) cc_final: 0.5642 (tmm) REVERT: R 97 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: R 175 MET cc_start: 0.5165 (OUTLIER) cc_final: 0.4129 (ptp) REVERT: R 181 MET cc_start: 0.4141 (ppp) cc_final: 0.3837 (pp-130) REVERT: R 232 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5502 (pp) REVERT: R 244 ILE cc_start: 0.7553 (mm) cc_final: 0.7087 (tp) REVERT: R 247 ARG cc_start: 0.7203 (ttp-110) cc_final: 0.6927 (mtm-85) REVERT: R 268 GLU cc_start: 0.6779 (mp0) cc_final: 0.6552 (mm-30) REVERT: R 342 GLU cc_start: 0.7784 (tp30) cc_final: 0.7430 (tp30) REVERT: R 381 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6192 (mp) REVERT: R 391 MET cc_start: 0.6245 (mtm) cc_final: 0.5842 (mmt) REVERT: L 71 ASP cc_start: 0.8516 (m-30) cc_final: 0.7956 (m-30) REVERT: L 135 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8550 (t) REVERT: L 171 LYS cc_start: 0.8464 (mptt) cc_final: 0.8149 (mmtt) outliers start: 34 outliers final: 28 residues processed: 127 average time/residue: 0.9780 time to fit residues: 132.8173 Evaluate side-chains 128 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 97 PHE Chi-restraints excluded: chain R residue 175 MET Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 234 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 381 ILE Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 416 HIS 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 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 165 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 221 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.204465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151122 restraints weight = 7369.460| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.45 r_work: 0.3253 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7445 Z= 0.190 Angle : 0.639 10.438 10134 Z= 0.322 Chirality : 0.044 0.239 1156 Planarity : 0.004 0.036 1275 Dihedral : 4.364 19.455 1020 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.40 % Allowed : 25.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 936 helix: 2.22 (0.28), residues: 345 sheet: -0.19 (0.30), residues: 282 loop : 0.10 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 117 HIS 0.003 0.001 HIS R 313 PHE 0.021 0.002 PHE R 48 TYR 0.022 0.002 TYR R 355 ARG 0.004 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 432) hydrogen bonds : angle 4.87117 ( 1278) SS BOND : bond 0.00301 ( 6) SS BOND : angle 2.38495 ( 12) covalent geometry : bond 0.00444 ( 7439) covalent geometry : angle 0.63411 (10122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7893.74 seconds wall clock time: 141 minutes 35.69 seconds (8495.69 seconds total)