Starting phenix.real_space_refine on Wed Sep 17 08:50:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lmo_63219/09_2025/9lmo_63219.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lmo_63219/09_2025/9lmo_63219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lmo_63219/09_2025/9lmo_63219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lmo_63219/09_2025/9lmo_63219.map" model { file = "/net/cci-nas-00/data/ceres_data/9lmo_63219/09_2025/9lmo_63219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lmo_63219/09_2025/9lmo_63219.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.038 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 29 5.16 5 C 4682 2.51 5 N 1248 2.21 5 O 1373 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: 7332 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "K" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} 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} Chain: "R" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3089 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.74, per 1000 atoms: 0.24 Number of scatterers: 7332 At special positions: 0 Unit cell: (66.96, 104.16, 142.29, 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 29 16.00 O 1373 8.00 N 1248 7.00 C 4682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.02 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: 0.51 Conformation dependent library (CDL) restraints added in 459.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 42.8% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.526A pdb=" N PHE H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 90 through 94 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 201 through 204 Processing helix chain 'H' and resid 215 through 218 Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.190A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.191A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'R' and resid 18 through 48 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 68 removed outlier: 4.420A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 80 removed outlier: 3.957A pdb=" N TRP R 73 " --> pdb=" O THR R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 121 removed outlier: 3.921A pdb=" N CYS R 90 " --> pdb=" O GLY R 86 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER R 104 " --> pdb=" O ASN R 100 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE R 105 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.539A pdb=" N PHE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 162 Processing helix chain 'R' and resid 180 through 188 Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 214 through 232 Processing helix chain 'R' and resid 239 through 257 Processing helix chain 'R' and resid 262 through 289 Processing helix chain 'R' and resid 290 through 299 Processing helix chain 'R' and resid 299 through 306 removed outlier: 3.609A pdb=" N THR R 303 " --> pdb=" O GLU R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 341 Processing helix chain 'R' and resid 341 through 354 Processing helix chain 'R' and resid 365 through 379 removed outlier: 3.786A pdb=" N ALA R 377 " --> pdb=" O HIS R 373 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE R 378 " --> pdb=" O SER R 374 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR R 379 " --> pdb=" O SER R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 381 through 386 Processing helix chain 'R' and resid 389 through 394 removed outlier: 3.877A pdb=" N ASN R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 408 removed outlier: 4.170A pdb=" N SER R 399 " --> pdb=" O GLU R 395 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.720A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.729A pdb=" N TYR H 116 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.328A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.328A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.648A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.547A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.747A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.419A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.419A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.692A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 156 Processing sheet with id=AB6, first strand: chain 'R' and resid 163 through 164 removed outlier: 4.559A pdb=" N PHE R 169 " --> pdb=" O ASN R 164 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1376 1.32 - 1.45: 2309 1.45 - 1.58: 3777 1.58 - 1.71: 11 1.71 - 1.84: 39 Bond restraints: 7512 Sorted by residual: bond pdb=" CB HIS L 200 " pdb=" CG HIS L 200 " ideal model delta sigma weight residual 1.497 1.352 0.145 1.40e-02 5.10e+03 1.07e+02 bond pdb=" CG GLN L 90 " pdb=" CD GLN L 90 " ideal model delta sigma weight residual 1.516 1.337 0.179 2.50e-02 1.60e+03 5.12e+01 bond pdb=" CB HIS H 214 " pdb=" CG HIS H 214 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.92e+01 bond pdb=" N PRO L 143 " pdb=" CD PRO L 143 " ideal model delta sigma weight residual 1.473 1.398 0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" CB ARG H 41 " pdb=" CG ARG H 41 " ideal model delta sigma weight residual 1.520 1.362 0.158 3.00e-02 1.11e+03 2.79e+01 ... (remaining 7507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 8974 2.38 - 4.77: 1049 4.77 - 7.15: 151 7.15 - 9.53: 26 9.53 - 11.92: 6 Bond angle restraints: 10206 Sorted by residual: angle pdb=" N ARG R 211 " pdb=" CA ARG R 211 " pdb=" C ARG R 211 " ideal model delta sigma weight residual 113.16 101.53 11.63 1.24e+00 6.50e-01 8.79e+01 angle pdb=" N GLU H 162 " pdb=" CA GLU H 162 " pdb=" C GLU H 162 " ideal model delta sigma weight residual 113.45 124.68 -11.23 1.39e+00 5.18e-01 6.52e+01 angle pdb=" N TRP K 111 " pdb=" CA TRP K 111 " pdb=" C TRP K 111 " ideal model delta sigma weight residual 113.38 122.95 -9.57 1.23e+00 6.61e-01 6.05e+01 angle pdb=" C PRO H 161 " pdb=" N GLU H 162 " pdb=" CA GLU H 162 " ideal model delta sigma weight residual 120.58 130.75 -10.17 1.32e+00 5.74e-01 5.93e+01 angle pdb=" N LYS R 210 " pdb=" CA LYS R 210 " pdb=" C LYS R 210 " ideal model delta sigma weight residual 113.18 104.63 8.55 1.21e+00 6.83e-01 4.99e+01 ... (remaining 10201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 4193 14.85 - 29.69: 191 29.69 - 44.54: 34 44.54 - 59.39: 20 59.39 - 74.23: 8 Dihedral angle restraints: 4446 sinusoidal: 1708 harmonic: 2738 Sorted by residual: dihedral pdb=" CD ARG R 162 " pdb=" NE ARG R 162 " pdb=" CZ ARG R 162 " pdb=" NH1 ARG R 162 " ideal model delta sinusoidal sigma weight residual 0.00 54.58 -54.58 1 1.00e+01 1.00e-02 4.04e+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 58.14 34.86 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CA PRO H 133 " pdb=" C PRO H 133 " pdb=" N SER H 134 " pdb=" CA SER H 134 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 4443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 721 0.068 - 0.136: 302 0.136 - 0.204: 83 0.204 - 0.271: 21 0.271 - 0.339: 4 Chirality restraints: 1131 Sorted by residual: chirality pdb=" CA SER L 8 " pdb=" N SER L 8 " pdb=" C SER L 8 " pdb=" CB SER L 8 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA LEU R 215 " pdb=" N LEU R 215 " pdb=" C LEU R 215 " pdb=" CB LEU R 215 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA TRP K 111 " pdb=" N TRP K 111 " pdb=" C TRP K 111 " pdb=" CB TRP K 111 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1128 not shown) Planarity restraints: 1294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 162 " 0.918 9.50e-02 1.11e+02 4.11e-01 1.02e+02 pdb=" NE ARG R 162 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG R 162 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG R 162 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG R 162 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 318 " -0.044 2.00e-02 2.50e+03 8.84e-02 7.81e+01 pdb=" C GLU R 318 " 0.153 2.00e-02 2.50e+03 pdb=" O GLU R 318 " -0.058 2.00e-02 2.50e+03 pdb=" N ARG R 319 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 104 " 0.069 2.00e-02 2.50e+03 4.04e-02 3.26e+01 pdb=" CG TYR K 104 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR K 104 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR K 104 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR K 104 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR K 104 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR K 104 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR K 104 " 0.066 2.00e-02 2.50e+03 ... (remaining 1291 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 24 2.49 - 3.09: 5351 3.09 - 3.69: 11140 3.69 - 4.30: 16330 4.30 - 4.90: 27015 Nonbonded interactions: 59860 Sorted by model distance: nonbonded pdb=" NZ LYS R 91 " pdb=" OD1 ASP R 156 " model vdw 1.882 3.120 nonbonded pdb=" N SER L 32 " pdb=" NZ LYS R 254 " model vdw 1.961 3.200 nonbonded pdb=" CG1 VAL H 198 " pdb=" OG SER H 202 " model vdw 2.070 3.460 nonbonded pdb=" O PRO R 122 " pdb=" NH2 ARG R 129 " model vdw 2.233 3.120 nonbonded pdb=" NE1 TRP R 83 " pdb=" OG SER R 89 " model vdw 2.283 3.120 ... (remaining 59855 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: 1.570 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.020 0.179 7518 Z= 1.060 Angle : 1.625 11.917 10218 Z= 1.081 Chirality : 0.083 0.339 1131 Planarity : 0.014 0.411 1294 Dihedral : 10.357 74.235 2670 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.49 % 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: 0.92 (0.27), residues: 927 helix: 0.06 (0.25), residues: 326 sheet: 1.53 (0.34), residues: 232 loop : 0.74 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 317 TYR 0.069 0.007 TYR K 104 PHE 0.040 0.004 PHE K 68 TRP 0.035 0.006 TRP K 111 HIS 0.013 0.002 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.01997 ( 7512) covalent geometry : angle 1.62267 (10206) SS BOND : bond 0.00678 ( 6) SS BOND : angle 3.17196 ( 12) hydrogen bonds : bond 0.13921 ( 418) hydrogen bonds : angle 6.91886 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.7979 (mp0) cc_final: 0.7385 (mp0) REVERT: H 31 ASN cc_start: 0.7930 (t0) cc_final: 0.7574 (t0) REVERT: H 225 VAL cc_start: 0.8477 (t) cc_final: 0.8055 (t) REVERT: K 101 ASP cc_start: 0.8072 (t0) cc_final: 0.7602 (t0) REVERT: K 102 THR cc_start: 0.9198 (p) cc_final: 0.8907 (t) REVERT: K 104 TYR cc_start: 0.8085 (m-80) cc_final: 0.7860 (m-10) REVERT: L 83 ASP cc_start: 0.8816 (m-30) cc_final: 0.8519 (m-30) REVERT: L 162 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8830 (mm-40) REVERT: L 169 ASP cc_start: 0.7890 (t70) cc_final: 0.7203 (t0) REVERT: L 187 ASP cc_start: 0.9010 (m-30) cc_final: 0.8765 (m-30) REVERT: L 212 ASN cc_start: 0.8077 (t0) cc_final: 0.7709 (t0) REVERT: R 51 GLU cc_start: 0.7663 (pt0) cc_final: 0.7206 (pt0) REVERT: R 78 LEU cc_start: 0.8657 (tp) cc_final: 0.8346 (tp) REVERT: R 79 HIS cc_start: 0.7816 (m90) cc_final: 0.7250 (m170) REVERT: R 132 LYS cc_start: 0.8308 (tttt) cc_final: 0.7667 (mmtt) REVERT: R 183 LEU cc_start: 0.9171 (mp) cc_final: 0.8966 (mm) REVERT: R 224 ASP cc_start: 0.8923 (m-30) cc_final: 0.8450 (m-30) REVERT: R 374 SER cc_start: 0.9086 (m) cc_final: 0.8706 (p) outliers start: 1 outliers final: 1 residues processed: 288 average time/residue: 0.1206 time to fit residues: 42.8524 Evaluate side-chains 175 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN R 165 HIS R 278 GLN R 373 HIS R 382 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.075355 restraints weight = 15469.598| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.15 r_work: 0.2897 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 7518 Z= 0.284 Angle : 0.747 8.168 10218 Z= 0.399 Chirality : 0.047 0.257 1131 Planarity : 0.006 0.069 1294 Dihedral : 5.314 40.790 1029 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.79 % Allowed : 10.72 % Favored : 84.49 % 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: 1.69 (0.28), residues: 927 helix: 1.70 (0.28), residues: 335 sheet: 1.49 (0.34), residues: 226 loop : 0.45 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 22 TYR 0.018 0.002 TYR R 24 PHE 0.022 0.003 PHE K 68 TRP 0.015 0.002 TRP H 117 HIS 0.009 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 7512) covalent geometry : angle 0.74636 (10206) SS BOND : bond 0.00482 ( 6) SS BOND : angle 1.32779 ( 12) hydrogen bonds : bond 0.04895 ( 418) hydrogen bonds : angle 5.18857 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8168 (mp0) cc_final: 0.7727 (mp0) REVERT: H 31 ASN cc_start: 0.8752 (t0) cc_final: 0.8174 (t0) REVERT: H 79 LYS cc_start: 0.9682 (mtpp) cc_final: 0.9464 (mtmm) REVERT: H 138 LEU cc_start: 0.9118 (mt) cc_final: 0.8875 (mp) REVERT: H 223 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8420 (tppp) REVERT: K 82 GLN cc_start: 0.8212 (mt0) cc_final: 0.7887 (mm110) REVERT: K 101 ASP cc_start: 0.8487 (t0) cc_final: 0.8220 (t0) REVERT: L 5 MET cc_start: 0.8872 (mmm) cc_final: 0.8511 (mtp) REVERT: L 18 ASP cc_start: 0.8630 (t0) cc_final: 0.8373 (m-30) REVERT: L 144 ARG cc_start: 0.8344 (tpt90) cc_final: 0.8122 (tpt-90) REVERT: L 187 ASP cc_start: 0.9408 (m-30) cc_final: 0.8906 (m-30) REVERT: R 47 GLN cc_start: 0.8582 (mt0) cc_final: 0.8379 (mt0) REVERT: R 48 GLN cc_start: 0.8430 (mt0) cc_final: 0.8074 (mt0) REVERT: R 49 ARG cc_start: 0.8018 (mmp80) cc_final: 0.7794 (mmp80) REVERT: R 51 GLU cc_start: 0.7835 (pt0) cc_final: 0.7465 (pt0) REVERT: R 91 LYS cc_start: 0.9196 (mttt) cc_final: 0.8912 (mttp) REVERT: R 132 LYS cc_start: 0.8739 (tttt) cc_final: 0.8176 (mmtt) REVERT: R 183 LEU cc_start: 0.9368 (mp) cc_final: 0.9166 (mm) REVERT: R 212 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7655 (ttp-110) REVERT: R 224 ASP cc_start: 0.8872 (m-30) cc_final: 0.8521 (m-30) REVERT: R 303 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9190 (p) outliers start: 38 outliers final: 23 residues processed: 221 average time/residue: 0.0956 time to fit residues: 27.3499 Evaluate side-chains 189 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 210 CYS Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 320 LEU Chi-restraints excluded: chain R residue 326 ILE Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 373 HIS Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN K 13 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3527 r_free = 0.3527 target = 0.099979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074702 restraints weight = 15316.136| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.14 r_work: 0.2896 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7518 Z= 0.211 Angle : 0.652 7.190 10218 Z= 0.345 Chirality : 0.044 0.278 1131 Planarity : 0.005 0.046 1294 Dihedral : 4.754 19.308 1027 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.66 % Allowed : 13.49 % Favored : 82.85 % 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: 1.82 (0.28), residues: 927 helix: 2.24 (0.28), residues: 335 sheet: 1.17 (0.34), residues: 230 loop : 0.33 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 31 TYR 0.024 0.002 TYR L 188 PHE 0.021 0.002 PHE L 211 TRP 0.012 0.001 TRP H 117 HIS 0.011 0.002 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 7512) covalent geometry : angle 0.65025 (10206) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.58764 ( 12) hydrogen bonds : bond 0.04341 ( 418) hydrogen bonds : angle 4.83584 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.7995 (mp0) cc_final: 0.7641 (mp0) REVERT: H 108 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8486 (mm-30) REVERT: H 138 LEU cc_start: 0.8956 (mt) cc_final: 0.8736 (mp) REVERT: K 82 GLN cc_start: 0.8314 (mt0) cc_final: 0.7972 (mm110) REVERT: L 18 ASP cc_start: 0.8660 (t0) cc_final: 0.8446 (m-30) REVERT: L 141 PHE cc_start: 0.4943 (t80) cc_final: 0.4174 (t80) REVERT: L 169 ASP cc_start: 0.8486 (t0) cc_final: 0.7903 (t0) REVERT: L 187 ASP cc_start: 0.9451 (m-30) cc_final: 0.8959 (m-30) REVERT: R 19 PHE cc_start: 0.7482 (t80) cc_final: 0.7257 (t80) REVERT: R 47 GLN cc_start: 0.8595 (mt0) cc_final: 0.8394 (mt0) REVERT: R 48 GLN cc_start: 0.8318 (mt0) cc_final: 0.8095 (mt0) REVERT: R 51 GLU cc_start: 0.7833 (pt0) cc_final: 0.7562 (pt0) REVERT: R 132 LYS cc_start: 0.8871 (tttt) cc_final: 0.8344 (mmtt) REVERT: R 212 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7924 (ttp-110) REVERT: R 224 ASP cc_start: 0.8836 (m-30) cc_final: 0.8545 (m-30) outliers start: 29 outliers final: 22 residues processed: 190 average time/residue: 0.0984 time to fit residues: 24.3752 Evaluate side-chains 167 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 320 LEU Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 406 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN K 13 GLN L 126 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3536 r_free = 0.3536 target = 0.100881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.075564 restraints weight = 15443.646| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.18 r_work: 0.2908 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7518 Z= 0.167 Angle : 0.607 7.423 10218 Z= 0.317 Chirality : 0.043 0.259 1131 Planarity : 0.005 0.047 1294 Dihedral : 4.560 19.835 1027 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.66 % Allowed : 13.62 % Favored : 82.72 % 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: 1.86 (0.29), residues: 927 helix: 2.45 (0.28), residues: 336 sheet: 0.93 (0.34), residues: 230 loop : 0.37 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 45 TYR 0.016 0.001 TYR R 355 PHE 0.020 0.002 PHE L 211 TRP 0.011 0.001 TRP H 117 HIS 0.006 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7512) covalent geometry : angle 0.60597 (10206) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.34365 ( 12) hydrogen bonds : bond 0.03908 ( 418) hydrogen bonds : angle 4.65697 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.7924 (mp0) cc_final: 0.7714 (mp0) REVERT: H 108 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8530 (mm-30) REVERT: K 44 GLU cc_start: 0.7732 (pm20) cc_final: 0.7031 (mm-30) REVERT: K 53 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7718 (mtm-85) REVERT: K 82 GLN cc_start: 0.8227 (mt0) cc_final: 0.7856 (mm110) REVERT: K 87 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8060 (mtmm) REVERT: L 141 PHE cc_start: 0.4920 (t80) cc_final: 0.4179 (t80) REVERT: L 187 ASP cc_start: 0.9469 (m-30) cc_final: 0.9018 (m-30) REVERT: R 19 PHE cc_start: 0.7454 (t80) cc_final: 0.7250 (t80) REVERT: R 48 GLN cc_start: 0.8315 (mt0) cc_final: 0.8073 (mt0) REVERT: R 49 ARG cc_start: 0.8250 (mmt180) cc_final: 0.7876 (mmp-170) REVERT: R 51 GLU cc_start: 0.7734 (pt0) cc_final: 0.7439 (pt0) REVERT: R 132 LYS cc_start: 0.8861 (tttt) cc_final: 0.8362 (mmtt) REVERT: R 212 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8141 (ttp-110) REVERT: R 224 ASP cc_start: 0.8848 (m-30) cc_final: 0.8541 (m-30) outliers start: 29 outliers final: 23 residues processed: 171 average time/residue: 0.0956 time to fit residues: 21.4571 Evaluate side-chains 168 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 256 THR Chi-restraints excluded: chain R residue 320 LEU Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 406 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN K 13 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3525 r_free = 0.3525 target = 0.100135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075000 restraints weight = 15273.389| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.19 r_work: 0.2895 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7518 Z= 0.168 Angle : 0.593 7.423 10218 Z= 0.308 Chirality : 0.042 0.233 1131 Planarity : 0.005 0.048 1294 Dihedral : 4.446 20.209 1027 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.91 % Allowed : 14.12 % Favored : 81.97 % 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: 1.86 (0.29), residues: 927 helix: 2.46 (0.28), residues: 341 sheet: 0.96 (0.33), residues: 236 loop : 0.27 (0.37), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 19 TYR 0.017 0.001 TYR R 355 PHE 0.023 0.002 PHE L 211 TRP 0.010 0.001 TRP H 117 HIS 0.005 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7512) covalent geometry : angle 0.59171 (10206) SS BOND : bond 0.00232 ( 6) SS BOND : angle 1.32690 ( 12) hydrogen bonds : bond 0.03756 ( 418) hydrogen bonds : angle 4.55567 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8547 (mm-30) REVERT: H 206 GLN cc_start: 0.9171 (tp40) cc_final: 0.8768 (tp-100) REVERT: H 208 TYR cc_start: 0.8757 (m-80) cc_final: 0.8456 (m-80) REVERT: K 39 GLN cc_start: 0.8183 (tt0) cc_final: 0.7490 (tm-30) REVERT: K 82 GLN cc_start: 0.8118 (mt0) cc_final: 0.7737 (tp40) REVERT: L 141 PHE cc_start: 0.4885 (t80) cc_final: 0.4196 (t80) REVERT: L 187 ASP cc_start: 0.9446 (m-30) cc_final: 0.8960 (m-30) REVERT: L 190 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8500 (pttm) REVERT: R 19 PHE cc_start: 0.7509 (t80) cc_final: 0.7268 (t80) REVERT: R 48 GLN cc_start: 0.8243 (mt0) cc_final: 0.7960 (mt0) REVERT: R 49 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7907 (mmp-170) REVERT: R 51 GLU cc_start: 0.7739 (pt0) cc_final: 0.7516 (pt0) REVERT: R 114 ASP cc_start: 0.9179 (t70) cc_final: 0.8972 (t70) REVERT: R 132 LYS cc_start: 0.8908 (tttt) cc_final: 0.8430 (mmtt) REVERT: R 212 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8272 (ttp-110) REVERT: R 224 ASP cc_start: 0.8837 (m-30) cc_final: 0.8512 (m-30) outliers start: 31 outliers final: 27 residues processed: 168 average time/residue: 0.0882 time to fit residues: 19.5035 Evaluate side-chains 172 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 256 THR Chi-restraints excluded: chain R residue 320 LEU Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 SER Chi-restraints excluded: chain R residue 406 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3512 r_free = 0.3512 target = 0.099122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074270 restraints weight = 15562.975| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.19 r_work: 0.2885 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7518 Z= 0.177 Angle : 0.599 6.906 10218 Z= 0.311 Chirality : 0.042 0.205 1131 Planarity : 0.005 0.049 1294 Dihedral : 4.386 20.499 1027 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.41 % Allowed : 15.01 % Favored : 80.58 % 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: 1.83 (0.29), residues: 927 helix: 2.50 (0.28), residues: 341 sheet: 0.92 (0.34), residues: 236 loop : 0.20 (0.37), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 31 TYR 0.020 0.001 TYR R 355 PHE 0.014 0.002 PHE H 35 TRP 0.010 0.001 TRP H 117 HIS 0.005 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 7512) covalent geometry : angle 0.59729 (10206) SS BOND : bond 0.00219 ( 6) SS BOND : angle 1.36617 ( 12) hydrogen bonds : bond 0.03796 ( 418) hydrogen bonds : angle 4.56267 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 206 GLN cc_start: 0.9200 (tp40) cc_final: 0.8799 (tp-100) REVERT: H 208 TYR cc_start: 0.8738 (m-80) cc_final: 0.8375 (m-80) REVERT: K 39 GLN cc_start: 0.8189 (tt0) cc_final: 0.7574 (tm-30) REVERT: K 82 GLN cc_start: 0.8049 (mt0) cc_final: 0.7822 (tp40) REVERT: K 87 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8091 (mttp) REVERT: L 141 PHE cc_start: 0.4859 (t80) cc_final: 0.4124 (t80) REVERT: L 187 ASP cc_start: 0.9489 (m-30) cc_final: 0.9050 (m-30) REVERT: L 190 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8540 (pttm) REVERT: R 48 GLN cc_start: 0.8263 (mt0) cc_final: 0.7996 (mt0) REVERT: R 49 ARG cc_start: 0.8250 (mmt180) cc_final: 0.7895 (mmp-170) REVERT: R 51 GLU cc_start: 0.7720 (pt0) cc_final: 0.7519 (pt0) REVERT: R 132 LYS cc_start: 0.8928 (tttt) cc_final: 0.8474 (mmtt) REVERT: R 212 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8491 (ttp-110) REVERT: R 224 ASP cc_start: 0.8836 (m-30) cc_final: 0.8524 (m-30) outliers start: 35 outliers final: 27 residues processed: 168 average time/residue: 0.0891 time to fit residues: 19.7055 Evaluate side-chains 170 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 256 THR Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 SER Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 406 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3508 r_free = 0.3508 target = 0.099209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073996 restraints weight = 15543.331| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.18 r_work: 0.2872 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7518 Z= 0.178 Angle : 0.599 8.147 10218 Z= 0.310 Chirality : 0.042 0.208 1131 Planarity : 0.005 0.049 1294 Dihedral : 4.355 20.769 1027 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.67 % Allowed : 15.51 % Favored : 79.82 % 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: 1.89 (0.29), residues: 927 helix: 2.61 (0.28), residues: 337 sheet: 0.76 (0.34), residues: 234 loop : 0.36 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 31 TYR 0.021 0.001 TYR R 355 PHE 0.014 0.002 PHE H 35 TRP 0.009 0.001 TRP H 117 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7512) covalent geometry : angle 0.59782 (10206) SS BOND : bond 0.00232 ( 6) SS BOND : angle 1.11962 ( 12) hydrogen bonds : bond 0.03790 ( 418) hydrogen bonds : angle 4.54163 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.7672 (mtp85) REVERT: H 206 GLN cc_start: 0.9227 (tp40) cc_final: 0.8883 (tp-100) REVERT: H 208 TYR cc_start: 0.8743 (m-80) cc_final: 0.8341 (m-80) REVERT: K 32 TYR cc_start: 0.7958 (m-80) cc_final: 0.7549 (m-80) REVERT: K 39 GLN cc_start: 0.8215 (tt0) cc_final: 0.7603 (tm-30) REVERT: K 87 LYS cc_start: 0.8364 (mtmt) cc_final: 0.8099 (mttp) REVERT: L 141 PHE cc_start: 0.4948 (t80) cc_final: 0.4199 (t80) REVERT: L 145 GLU cc_start: 0.8642 (mp0) cc_final: 0.8417 (mp0) REVERT: L 187 ASP cc_start: 0.9513 (m-30) cc_final: 0.9192 (m-30) REVERT: L 190 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8612 (pttm) REVERT: R 48 GLN cc_start: 0.8263 (mt0) cc_final: 0.7984 (mt0) REVERT: R 49 ARG cc_start: 0.8300 (mmt180) cc_final: 0.7955 (mmp-170) REVERT: R 132 LYS cc_start: 0.8936 (tttt) cc_final: 0.8475 (mmtt) REVERT: R 212 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8519 (ttp-110) REVERT: R 224 ASP cc_start: 0.8840 (m-30) cc_final: 0.8513 (m-30) outliers start: 37 outliers final: 28 residues processed: 169 average time/residue: 0.0854 time to fit residues: 19.1028 Evaluate side-chains 169 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 256 THR Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 380 SER Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 406 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN K 82 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3536 r_free = 0.3536 target = 0.101008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.076025 restraints weight = 15564.246| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.19 r_work: 0.2917 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7518 Z= 0.130 Angle : 0.580 8.392 10218 Z= 0.298 Chirality : 0.041 0.192 1131 Planarity : 0.005 0.046 1294 Dihedral : 4.272 20.093 1027 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.15 % Allowed : 17.53 % Favored : 79.32 % 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: 1.97 (0.29), residues: 927 helix: 2.69 (0.28), residues: 338 sheet: 0.73 (0.33), residues: 242 loop : 0.42 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 31 TYR 0.018 0.001 TYR R 355 PHE 0.019 0.001 PHE H 35 TRP 0.011 0.001 TRP H 168 HIS 0.003 0.001 HIS R 155 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7512) covalent geometry : angle 0.57914 (10206) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.98683 ( 12) hydrogen bonds : bond 0.03538 ( 418) hydrogen bonds : angle 4.40902 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 TYR cc_start: 0.9120 (m-80) cc_final: 0.8908 (m-80) REVERT: H 206 GLN cc_start: 0.9214 (tp40) cc_final: 0.8968 (tp-100) REVERT: K 39 GLN cc_start: 0.8193 (tt0) cc_final: 0.7658 (tm-30) REVERT: K 87 LYS cc_start: 0.8369 (mtmt) cc_final: 0.8028 (mtmm) REVERT: L 141 PHE cc_start: 0.4801 (t80) cc_final: 0.4163 (t80) REVERT: L 145 GLU cc_start: 0.8595 (mp0) cc_final: 0.8354 (mp0) REVERT: L 187 ASP cc_start: 0.9511 (m-30) cc_final: 0.9131 (m-30) REVERT: L 190 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8635 (pttm) REVERT: R 48 GLN cc_start: 0.8266 (mt0) cc_final: 0.7976 (mt0) REVERT: R 49 ARG cc_start: 0.8287 (mmt180) cc_final: 0.7952 (mmp-170) REVERT: R 132 LYS cc_start: 0.8932 (tttt) cc_final: 0.8478 (mmtt) REVERT: R 212 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8576 (ttp80) REVERT: R 224 ASP cc_start: 0.8838 (m-30) cc_final: 0.8513 (m-30) outliers start: 25 outliers final: 20 residues processed: 156 average time/residue: 0.0874 time to fit residues: 17.9882 Evaluate side-chains 160 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 406 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3535 r_free = 0.3535 target = 0.100930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076141 restraints weight = 15333.870| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.16 r_work: 0.2925 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7518 Z= 0.134 Angle : 0.579 8.269 10218 Z= 0.298 Chirality : 0.041 0.174 1131 Planarity : 0.005 0.046 1294 Dihedral : 4.212 20.421 1027 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.03 % Allowed : 17.65 % Favored : 79.32 % 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: 2.04 (0.29), residues: 927 helix: 2.76 (0.28), residues: 338 sheet: 0.75 (0.34), residues: 236 loop : 0.46 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 31 TYR 0.024 0.001 TYR R 355 PHE 0.015 0.001 PHE H 35 TRP 0.010 0.001 TRP H 168 HIS 0.003 0.001 HIS R 155 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7512) covalent geometry : angle 0.57880 (10206) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.95313 ( 12) hydrogen bonds : bond 0.03458 ( 418) hydrogen bonds : angle 4.33645 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 TYR cc_start: 0.9111 (m-80) cc_final: 0.8888 (m-80) REVERT: H 108 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8559 (mm-30) REVERT: H 206 GLN cc_start: 0.9157 (tp40) cc_final: 0.8715 (tm-30) REVERT: K 32 TYR cc_start: 0.7990 (m-80) cc_final: 0.7669 (m-80) REVERT: K 44 GLU cc_start: 0.7715 (pm20) cc_final: 0.7037 (mm-30) REVERT: K 87 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8186 (mttp) REVERT: L 141 PHE cc_start: 0.4760 (t80) cc_final: 0.4068 (t80) REVERT: L 187 ASP cc_start: 0.9527 (m-30) cc_final: 0.9256 (m-30) REVERT: L 190 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8667 (pttm) REVERT: R 48 GLN cc_start: 0.8254 (mt0) cc_final: 0.7949 (mt0) REVERT: R 49 ARG cc_start: 0.8294 (mmt180) cc_final: 0.7954 (mmp-170) REVERT: R 132 LYS cc_start: 0.8934 (tttt) cc_final: 0.8495 (mmtt) REVERT: R 212 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8602 (ttp80) REVERT: R 224 ASP cc_start: 0.8840 (m-30) cc_final: 0.8524 (m-30) outliers start: 24 outliers final: 20 residues processed: 156 average time/residue: 0.0871 time to fit residues: 17.8295 Evaluate side-chains 159 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 320 LEU Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 375 SER Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 406 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN L 91 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3561 r_free = 0.3561 target = 0.102659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077886 restraints weight = 15255.407| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.18 r_work: 0.2952 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7518 Z= 0.118 Angle : 0.577 8.609 10218 Z= 0.297 Chirality : 0.041 0.203 1131 Planarity : 0.004 0.045 1294 Dihedral : 4.129 19.775 1027 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.27 % Allowed : 18.79 % Favored : 78.94 % 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: 2.11 (0.29), residues: 927 helix: 2.82 (0.28), residues: 338 sheet: 0.75 (0.34), residues: 245 loop : 0.53 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 31 TYR 0.022 0.001 TYR R 355 PHE 0.025 0.001 PHE L 211 TRP 0.009 0.001 TRP H 168 HIS 0.003 0.001 HIS R 155 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7512) covalent geometry : angle 0.57640 (10206) SS BOND : bond 0.00159 ( 6) SS BOND : angle 1.00801 ( 12) hydrogen bonds : bond 0.03307 ( 418) hydrogen bonds : angle 4.24391 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1854 Ramachandran restraints generated. 927 Oldfield, 0 Emsley, 927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 108 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8543 (mm-30) REVERT: H 206 GLN cc_start: 0.8995 (tp40) cc_final: 0.8608 (tm-30) REVERT: K 32 TYR cc_start: 0.7979 (m-80) cc_final: 0.7731 (m-80) REVERT: K 44 GLU cc_start: 0.7621 (pm20) cc_final: 0.6990 (mm-30) REVERT: L 141 PHE cc_start: 0.4700 (t80) cc_final: 0.4072 (t80) REVERT: L 144 ARG cc_start: 0.8217 (tpt90) cc_final: 0.7885 (tpt90) REVERT: L 187 ASP cc_start: 0.9506 (m-30) cc_final: 0.9161 (m-30) REVERT: L 190 LYS cc_start: 0.9131 (mtmm) cc_final: 0.8776 (pttm) REVERT: R 45 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8768 (tp40) REVERT: R 49 ARG cc_start: 0.8280 (mmt180) cc_final: 0.7926 (mmp-170) REVERT: R 132 LYS cc_start: 0.8925 (tttt) cc_final: 0.8468 (mmtt) REVERT: R 212 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8687 (ttp80) REVERT: R 224 ASP cc_start: 0.8860 (m-30) cc_final: 0.8545 (m-30) outliers start: 18 outliers final: 17 residues processed: 159 average time/residue: 0.0898 time to fit residues: 18.9862 Evaluate side-chains 159 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 177 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 212 ARG Chi-restraints excluded: chain R residue 320 LEU Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 406 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 90 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN L 91 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 GLN ** 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 = 0.3563 r_free = 0.3563 target = 0.102411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077961 restraints weight = 15317.180| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.18 r_work: 0.2962 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.251 7518 Z= 0.243 Angle : 1.024 59.188 10218 Z= 0.584 Chirality : 0.046 0.614 1131 Planarity : 0.005 0.064 1294 Dihedral : 4.147 19.768 1027 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.27 % Allowed : 19.29 % Favored : 78.44 % Cbeta Deviations : 0.11 % 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: 2.11 (0.29), residues: 927 helix: 2.83 (0.28), residues: 338 sheet: 0.76 (0.34), residues: 245 loop : 0.53 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG K 67 TYR 0.020 0.001 TYR R 355 PHE 0.017 0.001 PHE H 35 TRP 0.009 0.001 TRP H 168 HIS 0.003 0.001 HIS R 155 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 7512) covalent geometry : angle 1.02376 (10206) SS BOND : bond 0.02981 ( 6) SS BOND : angle 0.92386 ( 12) hydrogen bonds : bond 0.03314 ( 418) hydrogen bonds : angle 4.26906 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.38 seconds wall clock time: 31 minutes 14.95 seconds (1874.95 seconds total)