Starting phenix.real_space_refine on Fri Dec 27 12:38:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9y_44392/12_2024/9b9y_44392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9y_44392/12_2024/9b9y_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_44392/12_2024/9b9y_44392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9y_44392/12_2024/9b9y_44392.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9y_44392/12_2024/9b9y_44392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9y_44392/12_2024/9b9y_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.35, per 1000 atoms: 0.70 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: 1.24 Conformation dependent library (CDL) restraints added in 573.9 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: 0.57 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: 1.50 Time building geometry restraints manager: 1.39 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: 0.490 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.590 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- 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 : 0.596 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: 0.1416 time to fit residues: 29.4034 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 : 0.572 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.561 Fit side-chains REVERT: R 230 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: R 277 MET cc_start: 0.8413 (tmm) cc_final: 0.8106 (tmm) REVERT: N 36 TRP cc_start: 0.9037 (m100) cc_final: 0.7366 (m100) REVERT: N 82 MET cc_start: 0.8631 (pmm) cc_final: 0.8417 (pmm) outliers start: 9 outliers final: 8 residues processed: 132 average time/residue: 0.1409 time to fit residues: 25.2133 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 : 0.548 ------------------------------------------------------------------------------- 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 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1779 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= 0.213 Angle : 0.561 8.144 6574 Z= 0.285 Chirality : 0.042 0.152 750 Planarity : 0.003 0.028 813 Dihedral : 4.485 33.561 670 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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 141 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: R 240 MET cc_start: 0.8751 (tmm) cc_final: 0.8049 (ttp) REVERT: R 277 MET cc_start: 0.8328 (tmm) cc_final: 0.7980 (tmm) REVERT: N 36 TRP cc_start: 0.9056 (m100) cc_final: 0.7595 (m100) outliers start: 13 outliers final: 10 residues processed: 134 average time/residue: 0.1411 time to fit residues: 25.0828 Evaluate side-chains 125 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 27 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 47 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1950 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= 0.201 Angle : 0.572 9.518 6574 Z= 0.282 Chirality : 0.042 0.165 750 Planarity : 0.003 0.030 813 Dihedral : 4.175 32.734 670 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.34 % Allowed : 14.93 % Favored : 81.73 % 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: 1.80 (0.34), residues: 597 helix: 2.37 (0.28), residues: 321 sheet: 1.89 (0.57), 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 0.006 0.001 TYR N 79 ARG 0.008 0.000 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 142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.503 Fit side-chains REVERT: R 277 MET cc_start: 0.8266 (tmm) cc_final: 0.7913 (tmm) REVERT: R 1107 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: N 36 TRP cc_start: 0.9060 (m100) cc_final: 0.7607 (m100) outliers start: 17 outliers final: 13 residues processed: 131 average time/residue: 0.1442 time to fit residues: 24.9497 Evaluate side-chains 130 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 1107 GLU 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 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4857 Z= 0.207 Angle : 0.579 8.546 6574 Z= 0.288 Chirality : 0.042 0.178 750 Planarity : 0.003 0.033 813 Dihedral : 3.922 32.269 670 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.32 % Allowed : 15.91 % Favored : 79.76 % 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: 2.42 (0.28), residues: 321 sheet: 2.01 (0.57), residues: 83 loop : -1.24 (0.43), residues: 193 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 R 268 TYR 0.006 0.001 TYR R 215 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 143 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.549 Fit side-chains REVERT: R 277 MET cc_start: 0.8255 (tmm) cc_final: 0.7890 (tmm) REVERT: R 1107 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: R 1195 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8839 (t80) REVERT: N 36 TRP cc_start: 0.9077 (m100) cc_final: 0.7623 (m100) outliers start: 22 outliers final: 18 residues processed: 129 average time/residue: 0.1385 time to fit residues: 23.8630 Evaluate side-chains 138 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 1107 GLU 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 382 CYS 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 Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4857 Z= 0.259 Angle : 0.603 8.810 6574 Z= 0.301 Chirality : 0.043 0.193 750 Planarity : 0.003 0.031 813 Dihedral : 3.926 32.654 670 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.72 % Allowed : 16.50 % Favored : 78.78 % 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: 1.81 (0.35), residues: 597 helix: 2.44 (0.28), residues: 321 sheet: 1.39 (0.52), residues: 100 loop : -1.37 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R1082 HIS 0.002 0.000 HIS R 219 PHE 0.007 0.001 PHE R 268 TYR 0.007 0.001 TYR R 215 ARG 0.005 0.000 ARG R 226 *********************** 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 141 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.575 Fit side-chains REVERT: R 103 MET cc_start: 0.7615 (mtm) cc_final: 0.7410 (mtm) REVERT: R 277 MET cc_start: 0.8273 (tmm) cc_final: 0.7969 (tmm) REVERT: R 1107 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: R 1195 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8877 (t80) REVERT: N 36 TRP cc_start: 0.9095 (m100) cc_final: 0.7598 (m100) REVERT: N 72 ASP cc_start: 0.8005 (t0) cc_final: 0.7565 (t0) REVERT: N 82 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8491 (pmm) outliers start: 24 outliers final: 18 residues processed: 126 average time/residue: 0.1373 time to fit residues: 23.2165 Evaluate side-chains 135 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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 1107 GLU 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 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 Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4857 Z= 0.335 Angle : 0.650 9.220 6574 Z= 0.324 Chirality : 0.045 0.195 750 Planarity : 0.003 0.035 813 Dihedral : 4.081 32.834 670 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.30 % Allowed : 17.09 % 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: 1.68 (0.34), residues: 597 helix: 2.39 (0.28), residues: 320 sheet: 1.21 (0.51), residues: 98 loop : -1.42 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 255 HIS 0.001 0.001 HIS N 124 PHE 0.007 0.001 PHE N 29 TYR 0.008 0.001 TYR R 215 ARG 0.007 0.001 ARG R 226 *********************** 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 151 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.571 Fit side-chains REVERT: R 176 ASP cc_start: 0.8322 (t70) cc_final: 0.7672 (t0) REVERT: R 277 MET cc_start: 0.8294 (tmm) cc_final: 0.7995 (tmm) REVERT: R 1107 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: R 1195 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8922 (t80) REVERT: R 371 MET cc_start: 0.7210 (tpt) cc_final: 0.6959 (tpp) REVERT: N 36 TRP cc_start: 0.9161 (m100) cc_final: 0.7589 (m100) REVERT: N 77 THR cc_start: 0.8557 (p) cc_final: 0.8341 (p) REVERT: N 82 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8502 (pmm) outliers start: 27 outliers final: 21 residues processed: 133 average time/residue: 0.1366 time to fit residues: 24.2094 Evaluate side-chains 142 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 1107 GLU Chi-restraints excluded: chain R residue 1119 SER 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 382 CYS 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 Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2309 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= 0.174 Angle : 0.600 9.101 6574 Z= 0.296 Chirality : 0.043 0.192 750 Planarity : 0.003 0.030 813 Dihedral : 4.026 32.323 670 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.93 % Allowed : 19.06 % Favored : 77.01 % 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: 2.44 (0.28), residues: 320 sheet: 1.32 (0.52), residues: 98 loop : -1.39 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 299 HIS 0.002 0.000 HIS R 219 PHE 0.005 0.001 PHE N 104 TYR 0.006 0.001 TYR R1109 ARG 0.006 0.000 ARG R 226 *********************** 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 149 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.627 Fit side-chains REVERT: R 135 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9246 (mm) REVERT: R 176 ASP cc_start: 0.8190 (t70) cc_final: 0.7361 (t0) REVERT: R 277 MET cc_start: 0.8254 (tmm) cc_final: 0.7877 (tmm) REVERT: R 1107 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: R 1195 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8965 (t80) REVERT: N 36 TRP cc_start: 0.9076 (m100) cc_final: 0.7569 (m100) REVERT: N 82 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8471 (pmm) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.1356 time to fit residues: 24.6675 Evaluate side-chains 139 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 135 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 264 CYS Chi-restraints excluded: chain R residue 1107 GLU Chi-restraints excluded: chain R residue 1119 SER 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 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 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4857 Z= 0.245 Angle : 0.651 9.113 6574 Z= 0.322 Chirality : 0.046 0.271 750 Planarity : 0.003 0.032 813 Dihedral : 4.050 32.662 670 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.13 % Allowed : 19.65 % 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: 1.72 (0.34), residues: 597 helix: 2.35 (0.28), residues: 321 sheet: 1.37 (0.51), residues: 98 loop : -1.37 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 299 HIS 0.001 0.000 HIS R 219 PHE 0.009 0.001 PHE N 67 TYR 0.007 0.001 TYR R 215 ARG 0.010 0.001 ARG R 230 *********************** 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 147 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.568 Fit side-chains REVERT: R 135 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9250 (mm) REVERT: R 176 ASP cc_start: 0.8278 (t70) cc_final: 0.7472 (t0) REVERT: R 277 MET cc_start: 0.8259 (tmm) cc_final: 0.7888 (tmm) REVERT: R 1107 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: R 1195 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8976 (t80) REVERT: R 375 ILE cc_start: 0.9348 (mm) cc_final: 0.9044 (pt) REVERT: N 36 TRP cc_start: 0.9100 (m100) cc_final: 0.7574 (m100) REVERT: N 82 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8331 (pmm) outliers start: 21 outliers final: 16 residues processed: 132 average time/residue: 0.1348 time to fit residues: 23.8581 Evaluate side-chains 145 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 135 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 264 CYS Chi-restraints excluded: chain R residue 1107 GLU Chi-restraints excluded: chain R residue 1119 SER 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 17 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 54 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2442 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= 0.200 Angle : 0.650 9.330 6574 Z= 0.320 Chirality : 0.045 0.245 750 Planarity : 0.003 0.045 813 Dihedral : 4.022 32.730 670 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.93 % Allowed : 20.63 % Favored : 75.44 % 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: 1.66 (0.34), residues: 597 helix: 2.34 (0.28), residues: 320 sheet: 1.30 (0.52), residues: 98 loop : -1.41 (0.44), residues: 179 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 0.005 0.001 PHE R1121 TYR 0.010 0.001 TYR N 79 ARG 0.005 0.000 ARG R 226 ********************** 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: 20 poor density : 128 time to evaluate : 0.563 Fit side-chains REVERT: R 135 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9255 (mm) REVERT: R 176 ASP cc_start: 0.8262 (t70) cc_final: 0.7448 (t0) REVERT: R 277 MET cc_start: 0.8288 (tmm) cc_final: 0.7891 (tmm) REVERT: R 1107 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: R 1195 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.9011 (t80) REVERT: N 36 TRP cc_start: 0.9076 (m100) cc_final: 0.7548 (m100) REVERT: N 82 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8312 (pmm) outliers start: 20 outliers final: 16 residues processed: 134 average time/residue: 0.1386 time to fit residues: 24.8707 Evaluate side-chains 145 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 135 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 264 CYS Chi-restraints excluded: chain R residue 1107 GLU Chi-restraints excluded: chain R residue 1119 SER 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 17 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 46 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.093379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.073049 restraints weight = 9860.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.075880 restraints weight = 5029.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077761 restraints weight = 3258.421| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4857 Z= 0.229 Angle : 0.660 9.236 6574 Z= 0.325 Chirality : 0.045 0.235 750 Planarity : 0.003 0.028 813 Dihedral : 4.046 32.829 670 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.13 % Allowed : 21.02 % Favored : 74.85 % 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: 1.60 (0.34), residues: 597 helix: 2.30 (0.28), residues: 320 sheet: 1.24 (0.51), residues: 98 loop : -1.46 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 241 HIS 0.003 0.001 HIS R 219 PHE 0.022 0.001 PHE R 268 TYR 0.022 0.001 TYR N 79 ARG 0.009 0.001 ARG R 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1258.30 seconds wall clock time: 23 minutes 40.07 seconds (1420.07 seconds total)