Starting phenix.real_space_refine on Fri Dec 27 22:43:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7shs_25135/12_2024/7shs_25135.cif Found real_map, /net/cci-nas-00/data/ceres_data/7shs_25135/12_2024/7shs_25135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7shs_25135/12_2024/7shs_25135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7shs_25135/12_2024/7shs_25135.map" model { file = "/net/cci-nas-00/data/ceres_data/7shs_25135/12_2024/7shs_25135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7shs_25135/12_2024/7shs_25135.cif" } resolution = 4.1 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= 0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4545 2.51 5 N 1092 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6873 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2291 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Restraints were copied for chains: C, B Time building chain proxies: 4.17, per 1000 atoms: 0.61 Number of scatterers: 6873 At special positions: 0 Unit cell: (90.96, 81.864, 84.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1188 8.00 N 1092 7.00 C 4545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.80 Conformation dependent library (CDL) restraints added in 880.2 milliseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 26 through 53 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.615A pdb=" N TYR A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 95 removed outlier: 3.807A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.574A pdb=" N MET A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 removed outlier: 3.843A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 159 removed outlier: 3.743A pdb=" N CYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 164 through 199 removed outlier: 3.920A pdb=" N TYR A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.845A pdb=" N LEU A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.587A pdb=" N ALA A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 26 through 53 Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.615A pdb=" N TYR B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.807A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.574A pdb=" N MET B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 131 removed outlier: 3.844A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 159 removed outlier: 3.744A pdb=" N CYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 164 through 199 removed outlier: 3.920A pdb=" N TYR B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.846A pdb=" N LEU B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.587A pdb=" N ALA B 248 " --> pdb=" O TRP B 244 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 26 through 53 Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.615A pdb=" N TYR C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 72 through 95 removed outlier: 3.808A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.573A pdb=" N MET C 117 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 131 removed outlier: 3.844A pdb=" N LEU C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 159 removed outlier: 3.744A pdb=" N CYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 164 through 199 removed outlier: 3.920A pdb=" N TYR C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.845A pdb=" N LEU C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 269 removed outlier: 3.588A pdb=" N ALA C 248 " --> pdb=" O TRP C 244 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 447 hydrogen bonds defined for protein. 1323 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: 1.55 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2076 1.35 - 1.46: 2092 1.46 - 1.58: 2864 1.58 - 1.70: 0 1.70 - 1.81: 72 Bond restraints: 7104 Sorted by residual: bond pdb=" CB MET C 82 " pdb=" CG MET C 82 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.93e-01 bond pdb=" CB MET A 82 " pdb=" CG MET A 82 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.90e-01 bond pdb=" CB MET B 82 " pdb=" CG MET B 82 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.49e-01 bond pdb=" C CYS B 120 " pdb=" N PRO B 121 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.36e-02 5.41e+03 7.28e-01 bond pdb=" CB MET C 186 " pdb=" CG MET C 186 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.21e-01 ... (remaining 7099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 9402 1.82 - 3.65: 201 3.65 - 5.47: 24 5.47 - 7.30: 12 7.30 - 9.12: 21 Bond angle restraints: 9660 Sorted by residual: angle pdb=" CB MET B 82 " pdb=" CG MET B 82 " pdb=" SD MET B 82 " ideal model delta sigma weight residual 112.70 121.82 -9.12 3.00e+00 1.11e-01 9.25e+00 angle pdb=" CB MET A 82 " pdb=" CG MET A 82 " pdb=" SD MET A 82 " ideal model delta sigma weight residual 112.70 121.80 -9.10 3.00e+00 1.11e-01 9.21e+00 angle pdb=" CB MET C 82 " pdb=" CG MET C 82 " pdb=" SD MET C 82 " ideal model delta sigma weight residual 112.70 121.79 -9.09 3.00e+00 1.11e-01 9.17e+00 angle pdb=" CB MET B 16 " pdb=" CG MET B 16 " pdb=" SD MET B 16 " ideal model delta sigma weight residual 112.70 120.62 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" CB MET A 16 " pdb=" CG MET A 16 " pdb=" SD MET A 16 " ideal model delta sigma weight residual 112.70 120.62 -7.92 3.00e+00 1.11e-01 6.96e+00 ... (remaining 9655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3602 17.70 - 35.40: 301 35.40 - 53.11: 36 53.11 - 70.81: 6 70.81 - 88.51: 12 Dihedral angle restraints: 3957 sinusoidal: 1491 harmonic: 2466 Sorted by residual: dihedral pdb=" CA ASP B 272 " pdb=" C ASP B 272 " pdb=" N GLU B 273 " pdb=" CA GLU B 273 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA ASP C 272 " pdb=" C ASP C 272 " pdb=" N GLU C 273 " pdb=" CA GLU C 273 " ideal model delta harmonic sigma weight residual -180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASP A 272 " pdb=" C ASP A 272 " pdb=" N GLU A 273 " pdb=" CA GLU A 273 " ideal model delta harmonic sigma weight residual -180.00 -164.10 -15.90 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 624 0.029 - 0.058: 212 0.058 - 0.087: 129 0.087 - 0.116: 31 0.116 - 0.145: 9 Chirality restraints: 1005 Sorted by residual: chirality pdb=" CA ASP A 253 " pdb=" N ASP A 253 " pdb=" C ASP A 253 " pdb=" CB ASP A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ASP B 253 " pdb=" N ASP B 253 " pdb=" C ASP B 253 " pdb=" CB ASP B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ASP C 253 " pdb=" N ASP C 253 " pdb=" C ASP C 253 " pdb=" CB ASP C 253 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1002 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 223 " 0.014 2.00e-02 2.50e+03 1.49e-02 5.51e+00 pdb=" CG TRP C 223 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 223 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 223 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 223 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 223 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 223 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 223 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 223 " 0.014 2.00e-02 2.50e+03 1.48e-02 5.50e+00 pdb=" CG TRP B 223 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 223 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 223 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 223 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 223 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 223 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 223 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 223 " -0.014 2.00e-02 2.50e+03 1.47e-02 5.39e+00 pdb=" CG TRP A 223 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 223 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 223 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 223 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 223 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 223 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 223 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 223 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 223 " 0.000 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2536 2.86 - 3.37: 7146 3.37 - 3.88: 11704 3.88 - 4.39: 12583 4.39 - 4.90: 21034 Nonbonded interactions: 55003 Sorted by model distance: nonbonded pdb=" OE2 GLU A 69 " pdb=" N ARG B 136 " model vdw 2.349 3.120 nonbonded pdb=" O ASP A 242 " pdb=" OG1 THR A 245 " model vdw 2.354 3.040 nonbonded pdb=" O ASP C 242 " pdb=" OG1 THR C 245 " model vdw 2.354 3.040 nonbonded pdb=" O ASP B 242 " pdb=" OG1 THR B 245 " model vdw 2.355 3.040 nonbonded pdb=" OE1 GLN C 192 " pdb=" NH2 ARG C 195 " model vdw 2.388 3.120 ... (remaining 54998 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.690 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7104 Z= 0.174 Angle : 0.740 9.123 9660 Z= 0.370 Chirality : 0.040 0.145 1005 Planarity : 0.005 0.050 1206 Dihedral : 13.648 88.509 2397 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.74 (0.27), residues: 843 helix: 0.85 (0.20), residues: 615 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 223 HIS 0.001 0.000 HIS C 210 PHE 0.014 0.001 PHE C 276 TYR 0.026 0.001 TYR A 156 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8266 (pmm) cc_final: 0.7989 (ppp) REVERT: A 126 ASP cc_start: 0.8657 (t0) cc_final: 0.8269 (t0) REVERT: A 158 GLU cc_start: 0.8676 (tp30) cc_final: 0.8259 (tm-30) REVERT: A 177 TRP cc_start: 0.8306 (m100) cc_final: 0.8093 (m100) REVERT: A 250 CYS cc_start: 0.8771 (m) cc_final: 0.8270 (m) REVERT: B 34 TRP cc_start: 0.6187 (m-10) cc_final: 0.5752 (m100) REVERT: B 182 TYR cc_start: 0.6720 (t80) cc_final: 0.6194 (t80) REVERT: B 240 ILE cc_start: 0.7110 (pt) cc_final: 0.6806 (tp) REVERT: B 246 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7445 (pp20) REVERT: B 254 ILE cc_start: 0.8982 (mm) cc_final: 0.8611 (mm) REVERT: B 260 TYR cc_start: 0.7404 (t80) cc_final: 0.7027 (t80) REVERT: C 70 GLU cc_start: 0.8353 (pm20) cc_final: 0.7873 (pm20) REVERT: C 72 ASN cc_start: 0.8193 (m-40) cc_final: 0.7823 (m-40) REVERT: C 130 GLN cc_start: 0.8802 (mm110) cc_final: 0.8102 (mm110) REVERT: C 246 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7804 (mm-30) REVERT: C 251 VAL cc_start: 0.9084 (m) cc_final: 0.8870 (t) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2456 time to fit residues: 70.3394 Evaluate side-chains 125 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.0020 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN B 9 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN C 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7104 Z= 0.212 Angle : 0.577 6.791 9660 Z= 0.307 Chirality : 0.040 0.139 1005 Planarity : 0.005 0.049 1206 Dihedral : 3.982 18.617 942 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.73 % 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: 2.06 (0.29), residues: 843 helix: 1.72 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.65 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 230 HIS 0.004 0.001 HIS C 249 PHE 0.021 0.002 PHE B 226 TYR 0.018 0.002 TYR C 193 ARG 0.004 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8495 (pmm) cc_final: 0.8104 (ppp) REVERT: A 126 ASP cc_start: 0.8742 (t0) cc_final: 0.8434 (t0) REVERT: A 131 LEU cc_start: 0.9369 (tp) cc_final: 0.9114 (tp) REVERT: A 250 CYS cc_start: 0.8683 (m) cc_final: 0.8424 (m) REVERT: B 34 TRP cc_start: 0.6321 (m-10) cc_final: 0.5842 (m100) REVERT: B 40 LEU cc_start: 0.9110 (mp) cc_final: 0.8509 (tp) REVERT: B 82 MET cc_start: 0.8358 (ttp) cc_final: 0.7989 (ttp) REVERT: B 110 ASN cc_start: 0.8728 (p0) cc_final: 0.7890 (p0) REVERT: B 117 MET cc_start: 0.8648 (mmp) cc_final: 0.8372 (mmm) REVERT: B 123 LEU cc_start: 0.9333 (mt) cc_final: 0.9124 (mt) REVERT: B 210 HIS cc_start: 0.7350 (m90) cc_final: 0.7063 (m90) REVERT: B 246 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7466 (pp20) REVERT: B 257 LYS cc_start: 0.8184 (mptt) cc_final: 0.7907 (mmmm) REVERT: B 260 TYR cc_start: 0.7669 (t80) cc_final: 0.7023 (t80) REVERT: C 71 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 72 ASN cc_start: 0.8329 (m-40) cc_final: 0.7794 (m-40) REVERT: C 88 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8189 (mtmm) REVERT: C 94 LEU cc_start: 0.7802 (mt) cc_final: 0.7173 (mt) REVERT: C 130 GLN cc_start: 0.8817 (mm110) cc_final: 0.8098 (mm110) REVERT: C 131 LEU cc_start: 0.9211 (tp) cc_final: 0.8945 (tp) REVERT: C 171 TYR cc_start: 0.7455 (t80) cc_final: 0.7110 (t80) REVERT: C 175 CYS cc_start: 0.8679 (m) cc_final: 0.8158 (p) REVERT: C 246 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7956 (mm-30) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1501 time to fit residues: 32.5806 Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 82 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN C 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7104 Z= 0.197 Angle : 0.561 7.480 9660 Z= 0.294 Chirality : 0.040 0.140 1005 Planarity : 0.004 0.053 1206 Dihedral : 3.930 18.326 942 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.14 % Allowed : 2.56 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.30), residues: 843 helix: 1.83 (0.21), residues: 606 sheet: None (None), residues: 0 loop : 0.47 (0.47), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 177 HIS 0.005 0.001 HIS C 249 PHE 0.017 0.002 PHE A 276 TYR 0.018 0.002 TYR C 46 ARG 0.003 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8527 (pmm) cc_final: 0.8156 (ppp) REVERT: A 126 ASP cc_start: 0.8688 (t0) cc_final: 0.8376 (t0) REVERT: A 131 LEU cc_start: 0.9394 (tp) cc_final: 0.9110 (tp) REVERT: B 10 MET cc_start: 0.8595 (mtm) cc_final: 0.8237 (mmt) REVERT: B 34 TRP cc_start: 0.6417 (m-10) cc_final: 0.5956 (m100) REVERT: B 40 LEU cc_start: 0.9148 (mp) cc_final: 0.8799 (tp) REVERT: B 82 MET cc_start: 0.8408 (ttp) cc_final: 0.8032 (ttm) REVERT: B 110 ASN cc_start: 0.8598 (p0) cc_final: 0.7645 (t0) REVERT: B 117 MET cc_start: 0.8616 (mmp) cc_final: 0.8335 (mmm) REVERT: B 123 LEU cc_start: 0.9386 (mt) cc_final: 0.8974 (tt) REVERT: B 210 HIS cc_start: 0.7413 (m90) cc_final: 0.7020 (m170) REVERT: B 257 LYS cc_start: 0.8230 (mptt) cc_final: 0.7969 (mmmm) REVERT: B 260 TYR cc_start: 0.7742 (t80) cc_final: 0.7252 (t80) REVERT: C 72 ASN cc_start: 0.8334 (m-40) cc_final: 0.8109 (m-40) REVERT: C 82 MET cc_start: 0.8472 (ttp) cc_final: 0.8114 (ttp) REVERT: C 88 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8274 (mtmm) REVERT: C 94 LEU cc_start: 0.7773 (mt) cc_final: 0.7150 (mt) REVERT: C 117 MET cc_start: 0.8368 (mmp) cc_final: 0.7418 (tpp) REVERT: C 127 LEU cc_start: 0.8871 (pp) cc_final: 0.8603 (pp) REVERT: C 130 GLN cc_start: 0.8779 (mm110) cc_final: 0.8141 (mm110) REVERT: C 171 TYR cc_start: 0.7799 (t80) cc_final: 0.6931 (t80) REVERT: C 175 CYS cc_start: 0.8696 (m) cc_final: 0.8496 (p) REVERT: C 230 TRP cc_start: 0.8647 (t60) cc_final: 0.7161 (t60) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.1472 time to fit residues: 30.7270 Evaluate side-chains 108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7104 Z= 0.265 Angle : 0.625 7.140 9660 Z= 0.339 Chirality : 0.043 0.138 1005 Planarity : 0.004 0.048 1206 Dihedral : 4.441 22.615 942 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.29), residues: 843 helix: 1.56 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.43 (0.44), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 177 HIS 0.009 0.002 HIS C 249 PHE 0.017 0.002 PHE B 226 TYR 0.024 0.002 TYR C 46 ARG 0.004 0.001 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8535 (pmm) cc_final: 0.8166 (ppp) REVERT: A 126 ASP cc_start: 0.8661 (t0) cc_final: 0.8410 (t0) REVERT: A 131 LEU cc_start: 0.9413 (tp) cc_final: 0.9066 (tp) REVERT: A 176 PHE cc_start: 0.8573 (t80) cc_final: 0.8315 (t80) REVERT: B 10 MET cc_start: 0.7986 (mtm) cc_final: 0.7659 (mmt) REVERT: B 108 PHE cc_start: 0.7772 (t80) cc_final: 0.7297 (t80) REVERT: B 110 ASN cc_start: 0.8396 (p0) cc_final: 0.7678 (t0) REVERT: B 117 MET cc_start: 0.8609 (mmp) cc_final: 0.8221 (mmm) REVERT: B 260 TYR cc_start: 0.7517 (t80) cc_final: 0.7168 (t80) REVERT: C 82 MET cc_start: 0.8501 (ttp) cc_final: 0.8253 (ttp) REVERT: C 88 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8139 (mtmm) REVERT: C 94 LEU cc_start: 0.7729 (mt) cc_final: 0.6815 (mt) REVERT: C 130 GLN cc_start: 0.8716 (mm110) cc_final: 0.7974 (mm110) REVERT: C 171 TYR cc_start: 0.8289 (t80) cc_final: 0.7937 (t80) REVERT: C 175 CYS cc_start: 0.8771 (m) cc_final: 0.8485 (p) REVERT: C 176 PHE cc_start: 0.8819 (t80) cc_final: 0.8454 (t80) REVERT: C 219 PHE cc_start: 0.8170 (m-10) cc_final: 0.7887 (m-10) REVERT: C 223 TRP cc_start: 0.8489 (m-90) cc_final: 0.7728 (m-90) REVERT: C 246 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7951 (mm-30) REVERT: C 260 TYR cc_start: 0.7810 (t80) cc_final: 0.7592 (t80) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1488 time to fit residues: 28.6206 Evaluate side-chains 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 72 optimal weight: 0.0970 chunk 20 optimal weight: 10.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7104 Z= 0.130 Angle : 0.526 7.717 9660 Z= 0.270 Chirality : 0.038 0.138 1005 Planarity : 0.003 0.041 1206 Dihedral : 3.879 17.675 942 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.30), residues: 843 helix: 1.81 (0.21), residues: 609 sheet: None (None), residues: 0 loop : 0.60 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 177 HIS 0.008 0.001 HIS C 210 PHE 0.016 0.001 PHE C 173 TYR 0.017 0.001 TYR A 156 ARG 0.002 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8522 (pmm) cc_final: 0.8166 (ppp) REVERT: A 126 ASP cc_start: 0.8597 (t0) cc_final: 0.8338 (t0) REVERT: A 131 LEU cc_start: 0.9410 (tp) cc_final: 0.9087 (tp) REVERT: A 148 MET cc_start: 0.8759 (ttt) cc_final: 0.8545 (ttt) REVERT: A 257 LYS cc_start: 0.9072 (mptt) cc_final: 0.8792 (mmtm) REVERT: B 9 GLN cc_start: 0.7756 (pp30) cc_final: 0.7300 (pp30) REVERT: B 10 MET cc_start: 0.7968 (mtm) cc_final: 0.7735 (mmt) REVERT: B 108 PHE cc_start: 0.7883 (t80) cc_final: 0.7401 (t80) REVERT: B 110 ASN cc_start: 0.8258 (p0) cc_final: 0.7764 (t0) REVERT: B 117 MET cc_start: 0.8501 (mmp) cc_final: 0.8224 (mmm) REVERT: B 123 LEU cc_start: 0.9457 (mt) cc_final: 0.9143 (tt) REVERT: B 210 HIS cc_start: 0.7663 (m90) cc_final: 0.7392 (m170) REVERT: B 257 LYS cc_start: 0.8030 (mptt) cc_final: 0.7658 (mmmm) REVERT: B 260 TYR cc_start: 0.7473 (t80) cc_final: 0.7249 (t80) REVERT: C 16 MET cc_start: 0.8363 (mmp) cc_final: 0.7641 (tpp) REVERT: C 69 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7681 (pm20) REVERT: C 82 MET cc_start: 0.8436 (ttp) cc_final: 0.8113 (ttp) REVERT: C 88 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8123 (mtmm) REVERT: C 94 LEU cc_start: 0.7565 (mt) cc_final: 0.6942 (mt) REVERT: C 117 MET cc_start: 0.8293 (mmp) cc_final: 0.6236 (tmm) REVERT: C 125 TYR cc_start: 0.8027 (t80) cc_final: 0.7747 (t80) REVERT: C 130 GLN cc_start: 0.8626 (mm110) cc_final: 0.8034 (mm110) REVERT: C 148 MET cc_start: 0.8671 (ttp) cc_final: 0.8168 (ttp) REVERT: C 171 TYR cc_start: 0.8295 (t80) cc_final: 0.7843 (t80) REVERT: C 175 CYS cc_start: 0.8857 (m) cc_final: 0.8390 (p) REVERT: C 246 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7968 (mm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1473 time to fit residues: 29.2505 Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7104 Z= 0.195 Angle : 0.567 8.875 9660 Z= 0.297 Chirality : 0.040 0.156 1005 Planarity : 0.004 0.049 1206 Dihedral : 3.970 17.564 942 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.30), residues: 843 helix: 2.01 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.80 (0.45), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 223 HIS 0.006 0.001 HIS C 210 PHE 0.022 0.002 PHE B 86 TYR 0.019 0.002 TYR C 46 ARG 0.003 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8512 (pmm) cc_final: 0.8143 (ppp) REVERT: A 126 ASP cc_start: 0.8605 (t0) cc_final: 0.8359 (t0) REVERT: A 131 LEU cc_start: 0.9411 (tp) cc_final: 0.9048 (tp) REVERT: A 257 LYS cc_start: 0.9188 (mptt) cc_final: 0.8896 (mmtm) REVERT: B 108 PHE cc_start: 0.8126 (t80) cc_final: 0.7789 (t80) REVERT: B 110 ASN cc_start: 0.8212 (p0) cc_final: 0.7931 (t0) REVERT: B 117 MET cc_start: 0.8530 (mmp) cc_final: 0.8196 (mmm) REVERT: B 257 LYS cc_start: 0.8137 (mptt) cc_final: 0.7907 (mmmt) REVERT: B 260 TYR cc_start: 0.7561 (t80) cc_final: 0.7232 (t80) REVERT: C 53 THR cc_start: 0.6886 (t) cc_final: 0.6597 (p) REVERT: C 82 MET cc_start: 0.8437 (ttp) cc_final: 0.8191 (ttp) REVERT: C 88 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8114 (mtmm) REVERT: C 94 LEU cc_start: 0.7636 (mt) cc_final: 0.7032 (mm) REVERT: C 117 MET cc_start: 0.8274 (mmp) cc_final: 0.7183 (tpp) REVERT: C 125 TYR cc_start: 0.8351 (t80) cc_final: 0.8044 (t80) REVERT: C 130 GLN cc_start: 0.8710 (mm110) cc_final: 0.8075 (mm110) REVERT: C 148 MET cc_start: 0.8585 (ttp) cc_final: 0.8170 (ppp) REVERT: C 171 TYR cc_start: 0.8421 (t80) cc_final: 0.8003 (t80) REVERT: C 175 CYS cc_start: 0.9033 (m) cc_final: 0.8671 (p) REVERT: C 176 PHE cc_start: 0.8776 (t80) cc_final: 0.8429 (t80) REVERT: C 246 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7948 (mm-30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1641 time to fit residues: 30.9972 Evaluate side-chains 107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 78 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7104 Z= 0.184 Angle : 0.562 8.148 9660 Z= 0.295 Chirality : 0.040 0.138 1005 Planarity : 0.004 0.049 1206 Dihedral : 3.924 17.660 942 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.14 % Allowed : 1.71 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.30), residues: 843 helix: 1.65 (0.21), residues: 618 sheet: None (None), residues: 0 loop : 0.60 (0.48), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 223 HIS 0.007 0.001 HIS C 210 PHE 0.019 0.001 PHE C 173 TYR 0.019 0.002 TYR A 156 ARG 0.002 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.8576 (t0) cc_final: 0.8322 (t0) REVERT: A 131 LEU cc_start: 0.9414 (tp) cc_final: 0.9046 (tp) REVERT: A 257 LYS cc_start: 0.9172 (mptt) cc_final: 0.8882 (mmtm) REVERT: B 9 GLN cc_start: 0.7852 (pp30) cc_final: 0.7631 (pp30) REVERT: B 82 MET cc_start: 0.8424 (ttm) cc_final: 0.7956 (mtm) REVERT: B 108 PHE cc_start: 0.8168 (t80) cc_final: 0.7862 (t80) REVERT: B 110 ASN cc_start: 0.8176 (p0) cc_final: 0.7948 (t0) REVERT: B 117 MET cc_start: 0.8503 (mmp) cc_final: 0.8277 (mmm) REVERT: B 260 TYR cc_start: 0.7513 (t80) cc_final: 0.7179 (t80) REVERT: C 17 ASP cc_start: 0.7868 (m-30) cc_final: 0.7254 (t0) REVERT: C 82 MET cc_start: 0.8449 (ttp) cc_final: 0.8157 (ttp) REVERT: C 88 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8082 (mtmm) REVERT: C 94 LEU cc_start: 0.7641 (mt) cc_final: 0.6959 (mt) REVERT: C 117 MET cc_start: 0.8237 (mmp) cc_final: 0.7128 (tpp) REVERT: C 125 TYR cc_start: 0.8367 (t80) cc_final: 0.8027 (t80) REVERT: C 130 GLN cc_start: 0.8671 (mm110) cc_final: 0.8012 (mm110) REVERT: C 171 TYR cc_start: 0.8606 (t80) cc_final: 0.8184 (t80) REVERT: C 175 CYS cc_start: 0.9022 (m) cc_final: 0.8704 (p) REVERT: C 176 PHE cc_start: 0.8814 (t80) cc_final: 0.8442 (t80) REVERT: C 246 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7979 (mm-30) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1590 time to fit residues: 29.8136 Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7104 Z= 0.143 Angle : 0.550 8.136 9660 Z= 0.281 Chirality : 0.039 0.141 1005 Planarity : 0.004 0.050 1206 Dihedral : 3.753 15.524 942 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.30), residues: 843 helix: 1.92 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 0.89 (0.46), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 223 HIS 0.003 0.001 HIS B 3 PHE 0.024 0.001 PHE C 219 TYR 0.022 0.001 TYR A 156 ARG 0.007 0.000 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.8514 (t0) cc_final: 0.8251 (t0) REVERT: A 131 LEU cc_start: 0.9415 (tp) cc_final: 0.9041 (tp) REVERT: A 257 LYS cc_start: 0.9212 (mptt) cc_final: 0.9006 (mmtm) REVERT: B 9 GLN cc_start: 0.7817 (pp30) cc_final: 0.7468 (pp30) REVERT: B 108 PHE cc_start: 0.8158 (t80) cc_final: 0.7811 (t80) REVERT: B 110 ASN cc_start: 0.8092 (p0) cc_final: 0.7830 (t0) REVERT: B 117 MET cc_start: 0.8490 (mmp) cc_final: 0.8286 (mmm) REVERT: B 123 LEU cc_start: 0.9501 (mt) cc_final: 0.9228 (tt) REVERT: B 127 LEU cc_start: 0.8744 (tt) cc_final: 0.8364 (tp) REVERT: B 260 TYR cc_start: 0.7481 (t80) cc_final: 0.6983 (t80) REVERT: C 17 ASP cc_start: 0.7672 (m-30) cc_final: 0.7072 (t0) REVERT: C 69 GLU cc_start: 0.8394 (pm20) cc_final: 0.7844 (mm-30) REVERT: C 82 MET cc_start: 0.8437 (ttp) cc_final: 0.7948 (ttp) REVERT: C 88 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8164 (mtmm) REVERT: C 94 LEU cc_start: 0.7466 (mt) cc_final: 0.7031 (mt) REVERT: C 125 TYR cc_start: 0.7999 (t80) cc_final: 0.7650 (t80) REVERT: C 130 GLN cc_start: 0.8655 (mm110) cc_final: 0.8011 (mm110) REVERT: C 171 TYR cc_start: 0.8586 (t80) cc_final: 0.8037 (t80) REVERT: C 175 CYS cc_start: 0.9052 (m) cc_final: 0.8688 (p) REVERT: C 176 PHE cc_start: 0.8701 (t80) cc_final: 0.8435 (t80) REVERT: C 219 PHE cc_start: 0.8297 (m-80) cc_final: 0.7919 (m-10) REVERT: C 223 TRP cc_start: 0.8594 (m-90) cc_final: 0.7833 (m-90) REVERT: C 246 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8030 (mm-30) REVERT: C 260 TYR cc_start: 0.7673 (t80) cc_final: 0.7472 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1637 time to fit residues: 29.9816 Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN C 3 HIS ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7104 Z= 0.172 Angle : 0.554 8.673 9660 Z= 0.289 Chirality : 0.039 0.146 1005 Planarity : 0.004 0.051 1206 Dihedral : 3.780 15.789 942 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.14 % Allowed : 0.71 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.30), residues: 843 helix: 1.74 (0.21), residues: 618 sheet: None (None), residues: 0 loop : 0.65 (0.48), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 34 HIS 0.008 0.001 HIS C 210 PHE 0.015 0.001 PHE C 173 TYR 0.021 0.001 TYR B 156 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8520 (pmm) cc_final: 0.8211 (ppp) REVERT: A 126 ASP cc_start: 0.8510 (t0) cc_final: 0.8283 (t0) REVERT: A 131 LEU cc_start: 0.9415 (tp) cc_final: 0.9033 (tp) REVERT: A 257 LYS cc_start: 0.9221 (mptt) cc_final: 0.8985 (mmtm) REVERT: B 9 GLN cc_start: 0.7846 (pp30) cc_final: 0.7623 (pp30) REVERT: B 108 PHE cc_start: 0.8230 (t80) cc_final: 0.7819 (t80) REVERT: B 110 ASN cc_start: 0.8163 (p0) cc_final: 0.7956 (t0) REVERT: B 117 MET cc_start: 0.8505 (mmp) cc_final: 0.8281 (mmm) REVERT: B 123 LEU cc_start: 0.9519 (mt) cc_final: 0.9262 (mt) REVERT: B 257 LYS cc_start: 0.8105 (mptt) cc_final: 0.7636 (mmtm) REVERT: B 258 SER cc_start: 0.8360 (t) cc_final: 0.8143 (p) REVERT: B 260 TYR cc_start: 0.7507 (t80) cc_final: 0.7185 (t80) REVERT: C 10 MET cc_start: 0.7278 (mmt) cc_final: 0.6943 (mmt) REVERT: C 17 ASP cc_start: 0.7796 (m-30) cc_final: 0.7263 (t0) REVERT: C 82 MET cc_start: 0.8441 (ttp) cc_final: 0.7961 (ttp) REVERT: C 94 LEU cc_start: 0.7590 (mt) cc_final: 0.6947 (mt) REVERT: C 117 MET cc_start: 0.8148 (mmp) cc_final: 0.7028 (tpp) REVERT: C 130 GLN cc_start: 0.8683 (mm110) cc_final: 0.7982 (mm110) REVERT: C 171 TYR cc_start: 0.8685 (t80) cc_final: 0.8063 (t80) REVERT: C 175 CYS cc_start: 0.9077 (m) cc_final: 0.8697 (p) REVERT: C 176 PHE cc_start: 0.8774 (t80) cc_final: 0.8438 (t80) REVERT: C 246 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8147 (mm-30) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1764 time to fit residues: 31.3345 Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7104 Z= 0.229 Angle : 0.614 8.969 9660 Z= 0.324 Chirality : 0.042 0.156 1005 Planarity : 0.004 0.050 1206 Dihedral : 4.048 17.497 942 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.29), residues: 843 helix: 1.44 (0.20), residues: 630 sheet: None (None), residues: 0 loop : 0.57 (0.47), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 34 HIS 0.008 0.002 HIS C 210 PHE 0.018 0.002 PHE C 217 TYR 0.021 0.002 TYR A 156 ARG 0.003 0.000 ARG B 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8559 (pmm) cc_final: 0.8250 (ppp) REVERT: A 126 ASP cc_start: 0.8518 (t0) cc_final: 0.8298 (t0) REVERT: A 131 LEU cc_start: 0.9419 (tp) cc_final: 0.9029 (tp) REVERT: A 176 PHE cc_start: 0.8484 (t80) cc_final: 0.8226 (t80) REVERT: A 257 LYS cc_start: 0.9179 (mptt) cc_final: 0.8885 (mmtm) REVERT: B 108 PHE cc_start: 0.8217 (t80) cc_final: 0.7834 (t80) REVERT: B 110 ASN cc_start: 0.8160 (p0) cc_final: 0.7939 (t0) REVERT: B 117 MET cc_start: 0.8535 (mmp) cc_final: 0.8117 (mmm) REVERT: B 119 THR cc_start: 0.7695 (p) cc_final: 0.7159 (p) REVERT: B 123 LEU cc_start: 0.9464 (mt) cc_final: 0.8792 (mt) REVERT: B 182 TYR cc_start: 0.7580 (t80) cc_final: 0.7342 (t80) REVERT: B 257 LYS cc_start: 0.8169 (mptt) cc_final: 0.7890 (mptt) REVERT: B 260 TYR cc_start: 0.7527 (t80) cc_final: 0.7211 (t80) REVERT: C 10 MET cc_start: 0.7189 (mmt) cc_final: 0.6427 (mmt) REVERT: C 17 ASP cc_start: 0.7853 (m-30) cc_final: 0.7268 (t0) REVERT: C 69 GLU cc_start: 0.8339 (pm20) cc_final: 0.7574 (mm-30) REVERT: C 82 MET cc_start: 0.8470 (ttp) cc_final: 0.8001 (ttp) REVERT: C 88 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8410 (mtmm) REVERT: C 94 LEU cc_start: 0.7612 (mt) cc_final: 0.6854 (mt) REVERT: C 130 GLN cc_start: 0.8736 (mm110) cc_final: 0.7949 (mm110) REVERT: C 171 TYR cc_start: 0.8731 (t80) cc_final: 0.8132 (t80) REVERT: C 175 CYS cc_start: 0.9024 (m) cc_final: 0.8681 (p) REVERT: C 176 PHE cc_start: 0.8892 (t80) cc_final: 0.8467 (t80) REVERT: C 250 CYS cc_start: 0.8842 (m) cc_final: 0.8383 (t) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1587 time to fit residues: 28.6830 Evaluate side-chains 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 58 optimal weight: 0.0060 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.074174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.066573 restraints weight = 31311.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068446 restraints weight = 17576.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069603 restraints weight = 11501.613| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7104 Z= 0.149 Angle : 0.563 8.234 9660 Z= 0.286 Chirality : 0.039 0.147 1005 Planarity : 0.003 0.049 1206 Dihedral : 3.726 15.060 942 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.30), residues: 843 helix: 1.68 (0.21), residues: 618 sheet: None (None), residues: 0 loop : 0.54 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 223 HIS 0.003 0.001 HIS A 249 PHE 0.022 0.001 PHE A 276 TYR 0.020 0.001 TYR A 156 ARG 0.003 0.000 ARG C 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1419.28 seconds wall clock time: 26 minutes 39.94 seconds (1599.94 seconds total)