Starting phenix.real_space_refine on Sat Apr 6 02:54:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpw_4616/04_2024/6qpw_4616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpw_4616/04_2024/6qpw_4616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpw_4616/04_2024/6qpw_4616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpw_4616/04_2024/6qpw_4616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpw_4616/04_2024/6qpw_4616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpw_4616/04_2024/6qpw_4616_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 4260 2.51 5 N 1187 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "B ARG 526": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 1014": "OE1" <-> "OE2" Residue "C GLU 1021": "OE1" <-> "OE2" Residue "C ASP 1028": "OD1" <-> "OD2" Residue "C PHE 1056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1057": "OE1" <-> "OE2" Residue "C ASP 1154": "OD1" <-> "OD2" Residue "C ARG 1187": "NH1" <-> "NH2" Residue "E GLU 1075": "OE1" <-> "OE2" Residue "E GLU 1115": "OE1" <-> "OE2" Residue "E GLU 1123": "OE1" <-> "OE2" Residue "E GLU 1128": "OE1" <-> "OE2" Residue "E GLU 1141": "OE1" <-> "OE2" Residue "E GLU 1142": "OE1" <-> "OE2" Residue "E PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1167": "OE1" <-> "OE2" Residue "E GLU 1198": "OE1" <-> "OE2" Residue "E ASP 1204": "OD1" <-> "OD2" Residue "E ARG 1216": "NH1" <-> "NH2" Residue "E PHE 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1246": "NH1" <-> "NH2" Residue "E ARG 1254": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1486 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain breaks: 2 Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "C" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2987 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 7, 'TRANS': 369} Chain breaks: 2 Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1610 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.45, per 1000 atoms: 0.66 Number of scatterers: 6784 At special positions: 0 Unit cell: (128.79, 103.68, 89.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 6 15.00 Mg 2 11.99 O 1305 8.00 N 1187 7.00 C 4260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C1159 " - pdb=" SG CYS E1201 " distance=2.04 Simple disulfide: pdb=" SG CYS C1204 " - pdb=" SG CYS E1160 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 7 sheets defined 43.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.828A pdb=" N GLU A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 205 through 233 Processing helix chain 'B' and resid 484 through 498 removed outlier: 4.046A pdb=" N GLU B 498 " --> pdb=" O LYS B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 512 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 521 through 536 Processing helix chain 'B' and resid 557 through 560 removed outlier: 3.577A pdb=" N PHE B 560 " --> pdb=" O PRO B 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 560' Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 58 through 64 Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 159 through 170 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 177 through 203 removed outlier: 4.663A pdb=" N GLN C 195 " --> pdb=" O GLN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1059 removed outlier: 3.760A pdb=" N SER C1043 " --> pdb=" O ASN C1039 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C1050 " --> pdb=" O GLN C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1145 removed outlier: 4.246A pdb=" N MET C1144 " --> pdb=" O LEU C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1162 through 1177 removed outlier: 4.094A pdb=" N LYS C1177 " --> pdb=" O LYS C1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1220 Processing helix chain 'E' and resid 1070 through 1125 removed outlier: 3.970A pdb=" N ALA E1109 " --> pdb=" O LEU E1105 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR E1118 " --> pdb=" O GLN E1114 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N HIS E1119 " --> pdb=" O GLU E1115 " (cutoff:3.500A) Processing helix chain 'E' and resid 1147 through 1149 No H-bonds generated for 'chain 'E' and resid 1147 through 1149' Processing helix chain 'E' and resid 1166 through 1168 No H-bonds generated for 'chain 'E' and resid 1166 through 1168' Processing helix chain 'E' and resid 1171 through 1186 Processing helix chain 'E' and resid 1205 through 1218 removed outlier: 3.511A pdb=" N GLU E1217 " --> pdb=" O LYS E1213 " (cutoff:3.500A) Processing helix chain 'E' and resid 1232 through 1237 removed outlier: 5.123A pdb=" N ALA E1237 " --> pdb=" O ALA E1233 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 18 through 22 removed outlier: 6.953A pdb=" N VAL A 122 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 7 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET A 120 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU A 9 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TRP A 118 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR A 145 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 501 through 503 Processing sheet with id= C, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.587A pdb=" N VAL C 81 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 6 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU C 79 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 8 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 77 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 1207 through 1210 removed outlier: 3.696A pdb=" N THR C1208 " --> pdb=" O LYS C1201 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C1196 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE C1181 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE C 30 " --> pdb=" O PHE C1181 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS C1183 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 1135 through 1140 Processing sheet with id= F, first strand: chain 'E' and resid 1193 through 1196 removed outlier: 6.025A pdb=" N GLN E1224 " --> pdb=" O PHE E1194 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU E1196 " --> pdb=" O GLN E1224 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE E1226 " --> pdb=" O LEU E1196 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 1240 through 1247 308 hydrogen bonds defined for protein. 900 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: 1.78 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 2313 1.37 - 1.52: 2354 1.52 - 1.66: 2181 1.66 - 1.81: 36 1.81 - 1.96: 3 Bond restraints: 6887 Sorted by residual: bond pdb=" C LEU C 91 " pdb=" N PRO C 92 " ideal model delta sigma weight residual 1.335 1.370 -0.034 1.30e-02 5.92e+03 6.97e+00 bond pdb=" CA THR B 514 " pdb=" CB THR B 514 " ideal model delta sigma weight residual 1.533 1.564 -0.031 1.82e-02 3.02e+03 2.96e+00 bond pdb=" N ASN C 119 " pdb=" CA ASN C 119 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.23e+00 bond pdb=" CG1 ILE E1113 " pdb=" CD1 ILE E1113 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C PRO E1190 " pdb=" N SER E1191 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.47e-02 4.63e+03 1.64e+00 ... (remaining 6882 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.40: 141 106.40 - 113.32: 3701 113.32 - 120.23: 2688 120.23 - 127.14: 2686 127.14 - 134.05: 50 Bond angle restraints: 9266 Sorted by residual: angle pdb=" N ALA C1141 " pdb=" CA ALA C1141 " pdb=" C ALA C1141 " ideal model delta sigma weight residual 113.12 105.66 7.46 1.25e+00 6.40e-01 3.56e+01 angle pdb=" CA CYS E1160 " pdb=" CB CYS E1160 " pdb=" SG CYS E1160 " ideal model delta sigma weight residual 114.40 127.18 -12.78 2.30e+00 1.89e-01 3.09e+01 angle pdb=" CA CYS C1204 " pdb=" CB CYS C1204 " pdb=" SG CYS C1204 " ideal model delta sigma weight residual 114.40 123.56 -9.16 2.30e+00 1.89e-01 1.58e+01 angle pdb=" N PHE A 12 " pdb=" CA PHE A 12 " pdb=" C PHE A 12 " ideal model delta sigma weight residual 110.53 105.83 4.70 1.29e+00 6.01e-01 1.33e+01 angle pdb=" C GLU C1203 " pdb=" N CYS C1204 " pdb=" CA CYS C1204 " ideal model delta sigma weight residual 122.06 115.41 6.65 1.86e+00 2.89e-01 1.28e+01 ... (remaining 9261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.50: 3739 18.50 - 36.99: 388 36.99 - 55.49: 87 55.49 - 73.98: 15 73.98 - 92.48: 8 Dihedral angle restraints: 4237 sinusoidal: 1791 harmonic: 2446 Sorted by residual: dihedral pdb=" CB CYS C1159 " pdb=" SG CYS C1159 " pdb=" SG CYS E1201 " pdb=" CB CYS E1201 " ideal model delta sinusoidal sigma weight residual -86.00 -21.71 -64.29 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CA PHE A 12 " pdb=" C PHE A 12 " pdb=" N LYS A 13 " pdb=" CA LYS A 13 " ideal model delta harmonic sigma weight residual 180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CB CYS C1204 " pdb=" SG CYS C1204 " pdb=" SG CYS E1160 " pdb=" CB CYS E1160 " ideal model delta sinusoidal sigma weight residual -86.00 -41.47 -44.53 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 4234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 675 0.046 - 0.093: 239 0.093 - 0.139: 88 0.139 - 0.186: 25 0.186 - 0.232: 7 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CB ILE C1221 " pdb=" CA ILE C1221 " pdb=" CG1 ILE C1221 " pdb=" CG2 ILE C1221 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA CYS C1204 " pdb=" N CYS C1204 " pdb=" C CYS C1204 " pdb=" CB CYS C1204 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE E1185 " pdb=" CA ILE E1185 " pdb=" CG1 ILE E1185 " pdb=" CG2 ILE E1185 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1031 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 493 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ARG B 493 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG B 493 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS B 494 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E1158 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO E1159 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO E1159 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E1159 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E1235 " -0.020 2.00e-02 2.50e+03 1.91e-02 6.38e+00 pdb=" CG PHE E1235 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E1235 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E1235 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE E1235 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E1235 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E1235 " 0.000 2.00e-02 2.50e+03 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 145 2.68 - 3.23: 6134 3.23 - 3.79: 10707 3.79 - 4.34: 14203 4.34 - 4.90: 22996 Nonbonded interactions: 54185 Sorted by model distance: nonbonded pdb="MG MG E1301 " pdb=" O3B AGS E1302 " model vdw 2.122 2.170 nonbonded pdb=" OE1 GLN A 177 " pdb="MG MG A 301 " model vdw 2.180 2.170 nonbonded pdb="MG MG A 301 " pdb=" O3B AGS A 302 " model vdw 2.185 2.170 nonbonded pdb=" OG SER A 199 " pdb=" O LEU E1105 " model vdw 2.275 2.440 nonbonded pdb=" O1B AGS E1302 " pdb=" O2G AGS E1302 " model vdw 2.303 2.440 ... (remaining 54180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.900 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.010 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.005 0.050 6887 Z= 0.343 Angle : 0.995 12.782 9266 Z= 0.559 Chirality : 0.058 0.232 1034 Planarity : 0.006 0.070 1191 Dihedral : 16.131 92.477 2641 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.14 % Allowed : 11.75 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.55 (0.24), residues: 823 helix: -2.36 (0.19), residues: 390 sheet: -0.73 (0.44), residues: 125 loop : -2.85 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 118 HIS 0.007 0.001 HIS C 66 PHE 0.043 0.003 PHE E1235 TYR 0.018 0.002 TYR A 157 ARG 0.005 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8462 (m) cc_final: 0.8142 (m) REVERT: A 186 GLN cc_start: 0.8482 (mt0) cc_final: 0.8149 (mt0) REVERT: A 193 ARG cc_start: 0.7032 (tpt-90) cc_final: 0.6655 (ttp-110) REVERT: C 1034 LYS cc_start: 0.4682 (mttt) cc_final: 0.4297 (ptmt) REVERT: E 1216 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7658 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2456 time to fit residues: 55.2441 Evaluate side-chains 102 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 74 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: A 41 ASN A 227 GLN B 513 ASN C 197 ASN C1125 GLN E1076 GLN E1248 GLN E1265 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6887 Z= 0.250 Angle : 0.658 10.641 9266 Z= 0.348 Chirality : 0.046 0.186 1034 Planarity : 0.004 0.054 1191 Dihedral : 7.892 74.580 946 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.46 % Allowed : 19.67 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.26), residues: 823 helix: -0.77 (0.24), residues: 390 sheet: -0.59 (0.44), residues: 122 loop : -2.56 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 133 HIS 0.003 0.001 HIS A 19 PHE 0.024 0.002 PHE E1235 TYR 0.012 0.002 TYR C 2 ARG 0.004 0.000 ARG C1058 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7091 (tpt-90) cc_final: 0.6721 (ttp-110) REVERT: C 30 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8233 (mp) REVERT: C 1064 THR cc_start: 0.7202 (m) cc_final: 0.6993 (p) outliers start: 18 outliers final: 6 residues processed: 123 average time/residue: 0.2076 time to fit residues: 33.2831 Evaluate side-chains 108 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS C1130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6887 Z= 0.228 Angle : 0.592 8.765 9266 Z= 0.315 Chirality : 0.044 0.141 1034 Planarity : 0.004 0.044 1191 Dihedral : 7.415 76.198 946 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.37 % Allowed : 19.40 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.28), residues: 823 helix: -0.13 (0.25), residues: 390 sheet: -0.51 (0.45), residues: 128 loop : -2.43 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 118 HIS 0.003 0.001 HIS A 19 PHE 0.023 0.002 PHE E1235 TYR 0.012 0.002 TYR C 2 ARG 0.005 0.000 ARG C1058 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7142 (tpt-90) cc_final: 0.6727 (ttp-110) REVERT: C 1064 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.7130 (p) REVERT: C 1130 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.5760 (tt0) outliers start: 32 outliers final: 20 residues processed: 129 average time/residue: 0.2246 time to fit residues: 38.4881 Evaluate side-chains 123 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1130 GLN Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1096 GLN Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1160 CYS Chi-restraints excluded: chain E residue 1226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6887 Z= 0.248 Angle : 0.597 7.735 9266 Z= 0.315 Chirality : 0.044 0.155 1034 Planarity : 0.004 0.040 1191 Dihedral : 7.318 76.147 946 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.78 % Allowed : 20.49 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.28), residues: 823 helix: 0.11 (0.26), residues: 387 sheet: -0.62 (0.45), residues: 132 loop : -2.24 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 118 HIS 0.003 0.001 HIS A 19 PHE 0.023 0.002 PHE E1235 TYR 0.013 0.002 TYR C 2 ARG 0.004 0.000 ARG E1126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7483 (ttt) REVERT: A 193 ARG cc_start: 0.7197 (tpt-90) cc_final: 0.6782 (ttp-110) REVERT: A 202 LEU cc_start: 0.7490 (tp) cc_final: 0.7268 (tp) REVERT: C 27 GLN cc_start: 0.7198 (tt0) cc_final: 0.6933 (tt0) REVERT: C 28 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7069 (p0) REVERT: C 1175 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7822 (mp) outliers start: 35 outliers final: 20 residues processed: 130 average time/residue: 0.2019 time to fit residues: 34.6756 Evaluate side-chains 125 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1096 GLN Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1150 SER Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1160 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 ASN C1130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6887 Z= 0.296 Angle : 0.617 7.633 9266 Z= 0.324 Chirality : 0.045 0.145 1034 Planarity : 0.004 0.037 1191 Dihedral : 7.306 76.090 946 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.92 % Allowed : 22.54 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.17 (0.29), residues: 823 helix: 0.18 (0.26), residues: 387 sheet: -0.53 (0.44), residues: 144 loop : -2.16 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 118 HIS 0.004 0.001 HIS A 19 PHE 0.024 0.002 PHE E1235 TYR 0.013 0.002 TYR C 2 ARG 0.005 0.000 ARG E1126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 105 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7492 (ttt) REVERT: A 193 ARG cc_start: 0.7199 (tpt-90) cc_final: 0.6818 (ttp-110) REVERT: C 28 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7044 (p0) REVERT: C 1130 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6144 (tt0) REVERT: C 1175 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7751 (mp) outliers start: 36 outliers final: 24 residues processed: 129 average time/residue: 0.1962 time to fit residues: 33.4937 Evaluate side-chains 129 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1130 GLN Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1139 ILE Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1150 SER Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1252 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 197 GLN B 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6887 Z= 0.323 Angle : 0.626 7.720 9266 Z= 0.330 Chirality : 0.045 0.159 1034 Planarity : 0.004 0.036 1191 Dihedral : 7.341 76.118 946 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.87 % Allowed : 23.09 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.29), residues: 823 helix: 0.20 (0.26), residues: 387 sheet: -0.49 (0.44), residues: 143 loop : -2.18 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 118 HIS 0.005 0.001 HIS A 19 PHE 0.025 0.002 PHE E1235 TYR 0.014 0.002 TYR C 116 ARG 0.005 0.000 ARG E1126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 100 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7349 (ttt) REVERT: A 193 ARG cc_start: 0.7191 (tpt-90) cc_final: 0.6743 (ttm-80) REVERT: A 204 TYR cc_start: 0.6484 (m-80) cc_final: 0.6255 (m-80) REVERT: C 27 GLN cc_start: 0.7240 (tt0) cc_final: 0.6942 (tt0) REVERT: C 28 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7014 (p0) REVERT: C 1175 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7786 (mp) REVERT: C 1214 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.5950 (tpm170) outliers start: 43 outliers final: 31 residues processed: 129 average time/residue: 0.2331 time to fit residues: 38.5696 Evaluate side-chains 134 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1139 ILE Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1190 MET Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1096 GLN Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1150 SER Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1252 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN B 513 ASN E1135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6887 Z= 0.242 Angle : 0.582 7.556 9266 Z= 0.310 Chirality : 0.044 0.147 1034 Planarity : 0.003 0.035 1191 Dihedral : 7.151 76.763 946 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.78 % Allowed : 24.45 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.29), residues: 823 helix: 0.44 (0.26), residues: 386 sheet: -0.47 (0.44), residues: 144 loop : -2.15 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 118 HIS 0.003 0.001 HIS A 19 PHE 0.023 0.002 PHE E1235 TYR 0.012 0.002 TYR C 116 ARG 0.005 0.000 ARG E1126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7390 (ttt) REVERT: A 193 ARG cc_start: 0.7135 (tpt-90) cc_final: 0.6696 (ttm-80) REVERT: A 204 TYR cc_start: 0.6388 (m-80) cc_final: 0.6136 (m-80) REVERT: A 212 GLU cc_start: 0.7841 (tt0) cc_final: 0.7080 (tp30) REVERT: A 214 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7833 (mp0) REVERT: C 27 GLN cc_start: 0.7222 (tt0) cc_final: 0.6945 (tt0) REVERT: C 28 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.6894 (p0) REVERT: C 1114 ASN cc_start: 0.7716 (p0) cc_final: 0.7478 (p0) REVERT: C 1175 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7687 (mp) REVERT: C 1214 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5931 (tpm170) outliers start: 35 outliers final: 27 residues processed: 132 average time/residue: 0.2070 time to fit residues: 35.8801 Evaluate side-chains 130 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1139 ILE Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1150 SER Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1252 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN C1039 ASN E1135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6887 Z= 0.283 Angle : 0.619 9.800 9266 Z= 0.323 Chirality : 0.044 0.166 1034 Planarity : 0.004 0.036 1191 Dihedral : 7.146 75.939 946 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.19 % Allowed : 25.82 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.29), residues: 823 helix: 0.46 (0.26), residues: 387 sheet: -0.37 (0.44), residues: 144 loop : -2.20 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 118 HIS 0.004 0.001 HIS A 19 PHE 0.024 0.002 PHE E1235 TYR 0.013 0.002 TYR C 116 ARG 0.005 0.000 ARG E1126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 104 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7411 (ttt) REVERT: A 193 ARG cc_start: 0.7182 (tpt-90) cc_final: 0.6733 (ttm-80) REVERT: A 212 GLU cc_start: 0.7823 (tt0) cc_final: 0.7035 (tp30) REVERT: C 27 GLN cc_start: 0.7298 (tt0) cc_final: 0.7041 (tt0) REVERT: C 28 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.6996 (p0) REVERT: C 1114 ASN cc_start: 0.7666 (p0) cc_final: 0.7447 (p0) REVERT: C 1175 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7719 (mp) REVERT: C 1214 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.5923 (tpm170) REVERT: E 1139 ASP cc_start: 0.7427 (t0) cc_final: 0.7225 (t0) outliers start: 38 outliers final: 32 residues processed: 129 average time/residue: 0.1934 time to fit residues: 33.3642 Evaluate side-chains 136 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1139 ILE Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1150 SER Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1252 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN C 62 GLN E1135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6887 Z= 0.259 Angle : 0.620 8.625 9266 Z= 0.324 Chirality : 0.044 0.162 1034 Planarity : 0.003 0.035 1191 Dihedral : 7.094 76.234 946 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.78 % Allowed : 26.23 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.30), residues: 823 helix: 0.54 (0.26), residues: 386 sheet: -0.46 (0.44), residues: 145 loop : -2.13 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 118 HIS 0.003 0.001 HIS A 19 PHE 0.024 0.002 PHE E1235 TYR 0.013 0.002 TYR C 116 ARG 0.006 0.000 ARG E1126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7390 (ttt) REVERT: A 193 ARG cc_start: 0.7162 (tpt-90) cc_final: 0.6721 (ttm-80) REVERT: A 212 GLU cc_start: 0.7793 (tt0) cc_final: 0.6992 (tp30) REVERT: C 28 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.6972 (p0) REVERT: C 102 GLU cc_start: 0.3901 (OUTLIER) cc_final: 0.3648 (pm20) REVERT: C 1214 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.5943 (tpm170) outliers start: 35 outliers final: 30 residues processed: 124 average time/residue: 0.1920 time to fit residues: 32.1791 Evaluate side-chains 133 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1139 ILE Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1150 SER Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6887 Z= 0.296 Angle : 0.657 9.793 9266 Z= 0.338 Chirality : 0.046 0.211 1034 Planarity : 0.004 0.036 1191 Dihedral : 7.160 75.753 946 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.92 % Allowed : 26.64 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.30), residues: 823 helix: 0.49 (0.26), residues: 386 sheet: -0.36 (0.44), residues: 143 loop : -2.21 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 118 HIS 0.004 0.001 HIS A 19 PHE 0.024 0.002 PHE E1235 TYR 0.013 0.002 TYR C 116 ARG 0.005 0.000 ARG E1126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7365 (ttt) REVERT: A 193 ARG cc_start: 0.7194 (tpt-90) cc_final: 0.6744 (ttm-80) REVERT: A 212 GLU cc_start: 0.7786 (tt0) cc_final: 0.7031 (tp30) REVERT: A 214 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7848 (mp0) REVERT: C 28 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.6950 (p0) REVERT: C 102 GLU cc_start: 0.3918 (OUTLIER) cc_final: 0.3656 (pm20) REVERT: C 1214 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.5998 (tpm170) outliers start: 36 outliers final: 31 residues processed: 125 average time/residue: 0.2045 time to fit residues: 34.9877 Evaluate side-chains 136 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 1064 THR Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain C residue 1112 SER Chi-restraints excluded: chain C residue 1122 HIS Chi-restraints excluded: chain C residue 1132 THR Chi-restraints excluded: chain C residue 1139 ILE Chi-restraints excluded: chain C residue 1193 VAL Chi-restraints excluded: chain C residue 1208 THR Chi-restraints excluded: chain C residue 1214 ARG Chi-restraints excluded: chain E residue 1081 PHE Chi-restraints excluded: chain E residue 1093 GLU Chi-restraints excluded: chain E residue 1140 ILE Chi-restraints excluded: chain E residue 1150 SER Chi-restraints excluded: chain E residue 1157 MET Chi-restraints excluded: chain E residue 1252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.184935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145470 restraints weight = 8932.348| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.71 r_work: 0.3799 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6887 Z= 0.285 Angle : 0.651 9.842 9266 Z= 0.334 Chirality : 0.046 0.188 1034 Planarity : 0.004 0.035 1191 Dihedral : 7.141 76.006 946 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.92 % Allowed : 26.78 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.30), residues: 823 helix: 0.52 (0.26), residues: 386 sheet: -0.32 (0.45), residues: 141 loop : -2.13 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 118 HIS 0.004 0.001 HIS A 19 PHE 0.024 0.002 PHE E1235 TYR 0.013 0.002 TYR C 116 ARG 0.005 0.000 ARG E1126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.55 seconds wall clock time: 33 minutes 55.15 seconds (2035.15 seconds total)