Starting phenix.real_space_refine on Tue Jan 14 00:50:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9y_44392/01_2025/9b9y_44392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9y_44392/01_2025/9b9y_44392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9y_44392/01_2025/9b9y_44392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9y_44392/01_2025/9b9y_44392.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9y_44392/01_2025/9b9y_44392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9y_44392/01_2025/9b9y_44392.cif" } resolution = 3.5 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= 0.003 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 S 32 5.16 5 Cl 1 4.86 5 C 3095 2.51 5 N 786 2.21 5 O 836 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4753 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3775 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 464} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'7DY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.21, per 1000 atoms: 0.68 Number of scatterers: 4753 At special positions: 0 Unit cell: (65.27, 88.81, 116.63, 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) Cl 1 17.00 S 32 16.00 F 3 9.00 O 836 8.00 N 786 7.00 C 3095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 579.0 milliseconds 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 5 sheets defined 61.1% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'R' and resid 104 through 109 removed outlier: 3.860A pdb=" N PHE R 108 " --> pdb=" O ASP R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 144 Processing helix chain 'R' and resid 144 through 149 Processing helix chain 'R' and resid 150 through 152 No H-bonds generated for 'chain 'R' and resid 150 through 152' Processing helix chain 'R' and resid 153 through 176 removed outlier: 3.910A pdb=" N GLY R 157 " --> pdb=" O TYR R 153 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER R 167 " --> pdb=" O ASP R 163 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE R 170 " --> pdb=" O GLY R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 220 Processing helix chain 'R' and resid 220 through 228 removed outlier: 4.667A pdb=" N LYS R 225 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG R 226 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 250 Processing helix chain 'R' and resid 251 through 254 Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.529A pdb=" N LEU R 260 " --> pdb=" O ASN R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 1005 removed outlier: 3.610A pdb=" N LEU R 276 " --> pdb=" O ASP R 272 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE R1002 " --> pdb=" O TRP R 299 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER R1005 " --> pdb=" O GLY R1001 " (cutoff:3.500A) Processing helix chain 'R' and resid 1006 through 1007 No H-bonds generated for 'chain 'R' and resid 1006 through 1007' Processing helix chain 'R' and resid 1008 through 1012 removed outlier: 3.657A pdb=" N TYR R1011 " --> pdb=" O ASN R1008 " (cutoff:3.500A) Processing helix chain 'R' and resid 1015 through 1027 Processing helix chain 'R' and resid 1047 through 1059 Processing helix chain 'R' and resid 1076 through 1090 Processing helix chain 'R' and resid 1101 through 1112 Processing helix chain 'R' and resid 1125 through 1134 removed outlier: 3.585A pdb=" N LEU R1134 " --> pdb=" O GLU R1130 " (cutoff:3.500A) Processing helix chain 'R' and resid 1145 through 1150 removed outlier: 3.834A pdb=" N ILE R1150 " --> pdb=" O LEU R1146 " (cutoff:3.500A) Processing helix chain 'R' and resid 1162 through 1177 Processing helix chain 'R' and resid 1181 through 1195 Processing helix chain 'R' and resid 1196 through 368 removed outlier: 3.779A pdb=" N ARG R 336 " --> pdb=" O SER R1196 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 372 through 383 Processing helix chain 'R' and resid 384 through 401 Proline residue: R 394 - end of helix removed outlier: 3.859A pdb=" N TYR R 397 " --> pdb=" O ASN R 393 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA R 398 " --> pdb=" O PRO R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 401 through 412 Processing sheet with id=AA1, first strand: chain 'R' and resid 1093 through 1096 removed outlier: 8.596A pdb=" N LYS R1094 " --> pdb=" O MET R1067 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE R1069 " --> pdb=" O LYS R1094 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE R1096 " --> pdb=" O PHE R1069 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE R1071 " --> pdb=" O ILE R1096 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL R1033 " --> pdb=" O ARG R1068 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE R1070 " --> pdb=" O VAL R1033 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE R1035 " --> pdb=" O ILE R1070 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE R1072 " --> pdb=" O PHE R1035 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE R1037 " --> pdb=" O ILE R1072 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR R1034 " --> pdb=" O PHE R1114 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE R1116 " --> pdb=" O THR R1034 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET R1036 " --> pdb=" O ILE R1116 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL R1115 " --> pdb=" O ILE R1139 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER R1141 " --> pdb=" O VAL R1115 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE R1117 " --> pdb=" O SER R1141 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL R1158 " --> pdb=" O PRO R1138 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA R1140 " --> pdb=" O VAL R1158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 12 through 13 removed outlier: 6.814A pdb=" N VAL N 12 " --> pdb=" O SER N 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.687A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLY N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET N 34 " --> pdb=" O GLY N 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 58 through 59 removed outlier: 6.687A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLY N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET N 34 " --> pdb=" O GLY N 50 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 864 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: 1.45 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 742 1.31 - 1.43: 1334 1.43 - 1.56: 2730 1.56 - 1.69: 0 1.69 - 1.82: 51 Bond restraints: 4857 Sorted by residual: bond pdb=" CBE 7DY R1201 " pdb=" NAI 7DY R1201 " ideal model delta sigma weight residual 1.152 1.455 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" CAQ 7DY R1201 " pdb=" NAG 7DY R1201 " ideal model delta sigma weight residual 1.343 1.457 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" CAX 7DY R1201 " pdb=" CBE 7DY R1201 " ideal model delta sigma weight residual 1.428 1.524 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CBD 7DY R1201 " pdb=" OAE 7DY R1201 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CBC 7DY R1201 " pdb="CLAA 7DY R1201 " ideal model delta sigma weight residual 1.736 1.784 -0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 4852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.89: 6573 13.89 - 27.78: 0 27.78 - 41.67: 0 41.67 - 55.55: 0 55.55 - 69.44: 1 Bond angle restraints: 6574 Sorted by residual: angle pdb=" CAX 7DY R1201 " pdb=" CBE 7DY R1201 " pdb=" NAI 7DY R1201 " ideal model delta sigma weight residual 180.00 110.56 69.44 3.00e+00 1.11e-01 5.36e+02 angle pdb=" N VAL N 48 " pdb=" CA VAL N 48 " pdb=" C VAL N 48 " ideal model delta sigma weight residual 110.72 115.30 -4.58 1.01e+00 9.80e-01 2.05e+01 angle pdb=" CB MET R1193 " pdb=" CG MET R1193 " pdb=" SD MET R1193 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CAQ 7DY R1201 " pdb=" CAP 7DY R1201 " pdb=" OAE 7DY R1201 " ideal model delta sigma weight residual 101.99 113.29 -11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N TYR R1109 " pdb=" CA TYR R1109 " pdb=" C TYR R1109 " ideal model delta sigma weight residual 111.28 108.05 3.23 1.09e+00 8.42e-01 8.77e+00 ... (remaining 6569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2570 17.95 - 35.90: 249 35.90 - 53.85: 45 53.85 - 71.79: 7 71.79 - 89.74: 2 Dihedral angle restraints: 2873 sinusoidal: 1135 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS R 257 " pdb=" SG CYS R 257 " pdb=" SG CYS R 264 " pdb=" CB CYS R 264 " ideal model delta sinusoidal sigma weight residual -86.00 -130.51 44.51 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 95 " pdb=" CB CYS N 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.69 37.31 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" C VAL N 48 " pdb=" N VAL N 48 " pdb=" CA VAL N 48 " pdb=" CB VAL N 48 " ideal model delta harmonic sigma weight residual -122.00 -131.44 9.44 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 2870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 652 0.069 - 0.137: 94 0.137 - 0.206: 2 0.206 - 0.274: 1 0.274 - 0.343: 1 Chirality restraints: 750 Sorted by residual: chirality pdb=" CB ILE N 28 " pdb=" CA ILE N 28 " pdb=" CG1 ILE N 28 " pdb=" CG2 ILE N 28 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA VAL N 48 " pdb=" N VAL N 48 " pdb=" C VAL N 48 " pdb=" CB VAL N 48 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA SER R1111 " pdb=" N SER R1111 " pdb=" C SER R1111 " pdb=" CB SER R1111 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 747 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAJ 7DY R1201 " 0.156 2.00e-02 2.50e+03 2.59e-01 1.51e+03 pdb=" CAM 7DY R1201 " 0.051 2.00e-02 2.50e+03 pdb=" CAR 7DY R1201 " -0.116 2.00e-02 2.50e+03 pdb=" CAS 7DY R1201 " 0.103 2.00e-02 2.50e+03 pdb=" CAX 7DY R1201 " -0.215 2.00e-02 2.50e+03 pdb=" CAY 7DY R1201 " 0.001 2.00e-02 2.50e+03 pdb=" CAZ 7DY R1201 " -0.158 2.00e-02 2.50e+03 pdb=" CBE 7DY R1201 " -0.393 2.00e-02 2.50e+03 pdb=" NAI 7DY R1201 " 0.573 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 112 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO R 113 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 113 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 104 " 0.014 2.00e-02 2.50e+03 1.39e-02 3.38e+00 pdb=" CG PHE N 104 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE N 104 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE N 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE N 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 104 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE N 104 " -0.002 2.00e-02 2.50e+03 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1284 2.81 - 3.33: 4582 3.33 - 3.86: 7769 3.86 - 4.38: 8615 4.38 - 4.90: 15216 Nonbonded interactions: 37466 Sorted by model distance: nonbonded pdb=" OG SER R 265 " pdb=" O PHE R 268 " model vdw 2.288 3.040 nonbonded pdb=" O ARG R 148 " pdb=" NH1 ARG R 230 " model vdw 2.320 3.120 nonbonded pdb=" NH1 ARG R 214 " pdb=" OD1 ASP R 338 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASP R 272 " pdb=" OG1 THR R 274 " model vdw 2.331 3.040 nonbonded pdb=" O GLY R 166 " pdb=" NAI 7DY R1201 " model vdw 2.345 3.120 ... (remaining 37461 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 group one per residue 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: 0.420 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.006 0.303 4857 Z= 0.314 Angle : 1.158 69.442 6574 Z= 0.479 Chirality : 0.048 0.343 750 Planarity : 0.010 0.259 813 Dihedral : 14.200 89.743 1751 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.20 % Allowed : 0.00 % Favored : 99.80 % 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: 0.65 (0.33), residues: 597 helix: 1.28 (0.27), residues: 312 sheet: 1.76 (0.58), residues: 81 loop : -1.49 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 36 HIS 0.003 0.000 HIS R 219 PHE 0.031 0.002 PHE N 104 TYR 0.012 0.001 TYR N 94 ARG 0.006 0.000 ARG R 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.499 Fit side-chains REVERT: R 135 LEU cc_start: 0.9409 (mm) cc_final: 0.9141 (mm) REVERT: R 139 CYS cc_start: 0.8651 (m) cc_final: 0.8363 (m) REVERT: R 256 ASN cc_start: 0.9270 (p0) cc_final: 0.8637 (p0) REVERT: R 277 MET cc_start: 0.8348 (tmm) cc_final: 0.8001 (tmm) REVERT: R 1168 ASN cc_start: 0.8852 (m110) cc_final: 0.8514 (m110) REVERT: R 1187 ASN cc_start: 0.8991 (m-40) cc_final: 0.8714 (m-40) REVERT: N 36 TRP cc_start: 0.9101 (m100) cc_final: 0.8123 (m100) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1426 time to fit residues: 29.3574 Evaluate side-chains 129 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** 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 = 0.3308 r_free = 0.3308 target = 0.093727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.073078 restraints weight = 9809.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.075883 restraints weight = 5004.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077774 restraints weight = 3279.802| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4857 Z= 0.287 Angle : 0.590 8.483 6574 Z= 0.301 Chirality : 0.043 0.168 750 Planarity : 0.004 0.037 813 Dihedral : 4.902 38.658 670 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.77 % Allowed : 12.38 % Favored : 85.85 % 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: 1.43 (0.34), residues: 597 helix: 2.04 (0.28), residues: 320 sheet: 1.88 (0.56), residues: 82 loop : -1.43 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 299 HIS 0.003 0.001 HIS R 219 PHE 0.015 0.001 PHE N 29 TYR 0.009 0.001 TYR R 215 ARG 0.006 0.001 ARG R 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.535 Fit side-chains REVERT: R 230 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: R 277 MET cc_start: 0.8398 (tmm) cc_final: 0.8097 (tmm) REVERT: N 36 TRP cc_start: 0.9030 (m100) cc_final: 0.7390 (m100) REVERT: N 82 MET cc_start: 0.8613 (pmm) cc_final: 0.8409 (pmm) outliers start: 9 outliers final: 8 residues processed: 132 average time/residue: 0.1319 time to fit residues: 23.5018 Evaluate side-chains 126 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 382 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 83 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.073405 restraints weight = 9845.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076316 restraints weight = 4929.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078279 restraints weight = 3184.487| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4857 Z= 0.219 Angle : 0.562 8.107 6574 Z= 0.286 Chirality : 0.042 0.153 750 Planarity : 0.003 0.027 813 Dihedral : 4.497 33.607 670 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.55 % Allowed : 15.13 % Favored : 82.32 % 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: 1.64 (0.34), residues: 597 helix: 2.24 (0.28), residues: 321 sheet: 1.74 (0.56), residues: 83 loop : -1.30 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 299 HIS 0.003 0.000 HIS R 219 PHE 0.010 0.001 PHE N 29 TYR 0.009 0.001 TYR R1109 ARG 0.004 0.000 ARG R 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.564 Fit side-chains REVERT: R 240 MET cc_start: 0.8768 (tmm) cc_final: 0.8056 (ttp) REVERT: R 277 MET cc_start: 0.8304 (tmm) cc_final: 0.7968 (tmm) REVERT: N 36 TRP cc_start: 0.9064 (m100) cc_final: 0.7613 (m100) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.1468 time to fit residues: 26.1173 Evaluate side-chains 126 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 382 CYS Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.074046 restraints weight = 9879.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.076966 restraints weight = 4971.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.078926 restraints weight = 3221.146| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4857 Z= 0.195 Angle : 0.565 8.374 6574 Z= 0.284 Chirality : 0.042 0.167 750 Planarity : 0.003 0.032 813 Dihedral : 4.159 32.704 670 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.54 % Allowed : 15.32 % Favored : 81.14 % 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: 1.78 (0.34), residues: 597 helix: 2.35 (0.28), residues: 321 sheet: 1.86 (0.56), residues: 83 loop : -1.27 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.008 0.001 PHE N 29 TYR 0.007 0.001 TYR R1109 ARG 0.010 0.001 ARG R 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.511 Fit side-chains REVERT: R 277 MET cc_start: 0.8225 (tmm) cc_final: 0.7880 (tmm) REVERT: N 36 TRP cc_start: 0.9053 (m100) cc_final: 0.7640 (m100) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.1418 time to fit residues: 24.5220 Evaluate side-chains 128 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 382 CYS Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 0 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.074693 restraints weight = 9992.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.077628 restraints weight = 5001.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079593 restraints weight = 3207.278| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4857 Z= 0.174 Angle : 0.573 8.341 6574 Z= 0.291 Chirality : 0.042 0.177 750 Planarity : 0.003 0.035 813 Dihedral : 3.926 32.286 670 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.95 % Allowed : 16.90 % Favored : 80.16 % 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: 1.87 (0.34), residues: 597 helix: 2.44 (0.28), residues: 319 sheet: 2.00 (0.56), residues: 83 loop : -1.28 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.007 0.001 PHE R 268 TYR 0.008 0.001 TYR R1109 ARG 0.009 0.000 ARG R 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.493 Fit side-chains REVERT: R 230 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7838 (mmt180) REVERT: R 277 MET cc_start: 0.8248 (tmm) cc_final: 0.7887 (tmm) REVERT: R 1195 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8856 (t80) REVERT: R 371 MET cc_start: 0.7062 (tpt) cc_final: 0.6826 (tpp) REVERT: N 36 TRP cc_start: 0.9027 (m100) cc_final: 0.7623 (m100) REVERT: N 82 MET cc_start: 0.8693 (pmm) cc_final: 0.8371 (pmm) outliers start: 15 outliers final: 12 residues processed: 131 average time/residue: 0.1334 time to fit residues: 23.4400 Evaluate side-chains 134 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.073805 restraints weight = 9904.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.076687 restraints weight = 5023.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078629 restraints weight = 3254.477| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4857 Z= 0.198 Angle : 0.582 8.648 6574 Z= 0.293 Chirality : 0.043 0.193 750 Planarity : 0.003 0.035 813 Dihedral : 3.855 32.270 670 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.93 % Allowed : 17.68 % Favored : 78.39 % 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: 1.92 (0.34), residues: 597 helix: 2.48 (0.28), residues: 319 sheet: 2.08 (0.56), residues: 83 loop : -1.28 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 241 HIS 0.002 0.000 HIS R 219 PHE 0.012 0.001 PHE N 29 TYR 0.007 0.001 TYR R1109 ARG 0.007 0.000 ARG R 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: R 277 MET cc_start: 0.8271 (tmm) cc_final: 0.7899 (tmm) REVERT: R 1195 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8902 (t80) REVERT: N 36 TRP cc_start: 0.9050 (m100) cc_final: 0.7650 (m100) REVERT: N 82 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8335 (pmm) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.1389 time to fit residues: 23.8936 Evaluate side-chains 135 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 1158 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.073961 restraints weight = 9746.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.076772 restraints weight = 4949.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078650 restraints weight = 3239.774| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4857 Z= 0.196 Angle : 0.601 9.100 6574 Z= 0.299 Chirality : 0.043 0.194 750 Planarity : 0.003 0.033 813 Dihedral : 3.853 31.778 670 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.54 % Allowed : 18.86 % Favored : 77.60 % 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: 1.89 (0.34), residues: 597 helix: 2.44 (0.28), residues: 319 sheet: 2.07 (0.56), residues: 83 loop : -1.26 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.009 0.001 PHE N 29 TYR 0.006 0.001 TYR R1109 ARG 0.005 0.000 ARG R 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.586 Fit side-chains REVERT: R 277 MET cc_start: 0.8258 (tmm) cc_final: 0.7882 (tmm) REVERT: R 1107 GLU cc_start: 0.8791 (pm20) cc_final: 0.8413 (pm20) REVERT: R 1195 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8955 (t80) REVERT: N 36 TRP cc_start: 0.9051 (m100) cc_final: 0.7659 (m100) REVERT: N 82 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8379 (pmm) REVERT: N 117 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8478 (tp-100) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 0.1447 time to fit residues: 24.7911 Evaluate side-chains 134 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 1158 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.074032 restraints weight = 9877.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.076919 restraints weight = 4958.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.078879 restraints weight = 3214.667| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4857 Z= 0.192 Angle : 0.610 8.899 6574 Z= 0.301 Chirality : 0.044 0.213 750 Planarity : 0.003 0.032 813 Dihedral : 3.884 31.622 670 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.73 % Allowed : 19.65 % Favored : 76.62 % 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: 1.94 (0.35), residues: 597 helix: 2.47 (0.28), residues: 319 sheet: 2.17 (0.57), residues: 81 loop : -1.23 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.007 0.001 PHE N 29 TYR 0.005 0.001 TYR R 215 ARG 0.009 0.000 ARG R 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: R 135 LEU cc_start: 0.9502 (mm) cc_final: 0.9266 (mm) REVERT: R 176 ASP cc_start: 0.8195 (t70) cc_final: 0.7790 (t0) REVERT: R 277 MET cc_start: 0.8291 (tmm) cc_final: 0.7906 (tmm) REVERT: R 1195 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8977 (t80) REVERT: R 371 MET cc_start: 0.7086 (tpt) cc_final: 0.6812 (tpp) REVERT: N 36 TRP cc_start: 0.9049 (m100) cc_final: 0.7643 (m100) REVERT: N 72 ASP cc_start: 0.7977 (t0) cc_final: 0.7614 (t0) REVERT: N 82 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8359 (pmm) outliers start: 19 outliers final: 16 residues processed: 132 average time/residue: 0.1408 time to fit residues: 24.6918 Evaluate side-chains 141 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 1158 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 55 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.072644 restraints weight = 9965.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.075450 restraints weight = 5028.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.077370 restraints weight = 3260.032| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4857 Z= 0.248 Angle : 0.658 8.940 6574 Z= 0.323 Chirality : 0.045 0.239 750 Planarity : 0.003 0.035 813 Dihedral : 4.022 32.334 670 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.93 % Allowed : 18.86 % Favored : 77.21 % 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: 1.76 (0.34), residues: 597 helix: 2.43 (0.28), residues: 319 sheet: 1.48 (0.51), residues: 98 loop : -1.48 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R1082 HIS 0.003 0.001 HIS R 219 PHE 0.011 0.001 PHE N 29 TYR 0.013 0.001 TYR N 79 ARG 0.009 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: R 116 GLN cc_start: 0.7968 (mp-120) cc_final: 0.7401 (mp10) REVERT: R 135 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9228 (mm) REVERT: R 176 ASP cc_start: 0.8232 (t70) cc_final: 0.7397 (t0) REVERT: R 226 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7353 (ttt-90) REVERT: R 277 MET cc_start: 0.8281 (tmm) cc_final: 0.7924 (tmm) REVERT: R 1195 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8986 (t80) REVERT: R 371 MET cc_start: 0.7091 (tpt) cc_final: 0.6819 (tpp) REVERT: N 36 TRP cc_start: 0.9098 (m100) cc_final: 0.7671 (m100) REVERT: N 82 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8417 (pmm) outliers start: 20 outliers final: 17 residues processed: 131 average time/residue: 0.1487 time to fit residues: 25.5313 Evaluate side-chains 141 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 1158 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 chunk 4 optimal weight: 0.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.073886 restraints weight = 9582.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.076822 restraints weight = 4868.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.078828 restraints weight = 3158.528| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4857 Z= 0.194 Angle : 0.650 9.143 6574 Z= 0.318 Chirality : 0.044 0.221 750 Planarity : 0.003 0.029 813 Dihedral : 4.019 32.598 670 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.54 % Allowed : 19.65 % Favored : 76.82 % 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: 1.75 (0.34), residues: 597 helix: 2.46 (0.28), residues: 319 sheet: 1.42 (0.52), residues: 98 loop : -1.52 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.009 0.001 PHE N 29 TYR 0.013 0.001 TYR N 79 ARG 0.008 0.000 ARG R 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1194 Ramachandran restraints generated. 597 Oldfield, 0 Emsley, 597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.557 Fit side-chains REVERT: R 116 GLN cc_start: 0.7991 (mp-120) cc_final: 0.7722 (mp10) REVERT: R 135 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9241 (mm) REVERT: R 176 ASP cc_start: 0.8269 (t70) cc_final: 0.7439 (t0) REVERT: R 226 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7348 (ttt-90) REVERT: R 277 MET cc_start: 0.8316 (tmm) cc_final: 0.7906 (tmm) REVERT: R 1107 GLU cc_start: 0.8723 (pm20) cc_final: 0.8342 (pm20) REVERT: R 1195 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.9015 (t80) REVERT: N 6 GLU cc_start: 0.8201 (pm20) cc_final: 0.7313 (pm20) REVERT: N 36 TRP cc_start: 0.9084 (m100) cc_final: 0.7626 (m100) REVERT: N 82 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8402 (pmm) REVERT: N 114 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8403 (mp10) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.1462 time to fit residues: 26.0011 Evaluate side-chains 141 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 264 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 1158 VAL Chi-restraints excluded: chain R residue 1195 PHE Chi-restraints excluded: chain R residue 381 PHE Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.073573 restraints weight = 9694.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.076512 restraints weight = 4887.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.078511 restraints weight = 3150.977| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4857 Z= 0.208 Angle : 0.653 9.056 6574 Z= 0.320 Chirality : 0.045 0.224 750 Planarity : 0.003 0.031 813 Dihedral : 3.997 32.745 670 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.73 % Allowed : 19.45 % Favored : 76.82 % 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: 1.71 (0.34), residues: 597 helix: 2.46 (0.28), residues: 319 sheet: 1.35 (0.51), residues: 98 loop : -1.58 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP R 299 HIS 0.001 0.000 HIS R 181 PHE 0.009 0.001 PHE N 29 TYR 0.026 0.001 TYR N 79 ARG 0.008 0.001 ARG R 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1662.81 seconds wall clock time: 30 minutes 46.46 seconds (1846.46 seconds total)