Starting phenix.real_space_refine on Sun Mar 10 16:11:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/03_2024/7x83_33054.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/03_2024/7x83_33054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/03_2024/7x83_33054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/03_2024/7x83_33054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/03_2024/7x83_33054.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/03_2024/7x83_33054.pdb" } resolution = 3.4 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= 0.003 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 122": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 2.27, per 1000 atoms: 0.70 Number of scatterers: 3258 At special positions: 0 Unit cell: (100.43, 100.43, 35.69, 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 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 593.4 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.705A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 6.653A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 removed outlier: 6.553A pdb=" N TYR B 143 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 removed outlier: 6.958A pdb=" N LEU B 150 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 156 removed outlier: 6.509A pdb=" N ASN B 155 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 164 removed outlier: 6.916A pdb=" N GLU B 163 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.584A pdb=" N GLN B 168 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.541A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 192 removed outlier: 6.479A pdb=" N LEU B 190 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 213 removed outlier: 8.933A pdb=" N VAL B 202 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLU A 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA B 204 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N MET A 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR A 209 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER B 208 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR A 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET B 210 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE A 213 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 212 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 202 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 203 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA C 204 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 216 through 219 removed outlier: 5.914A pdb=" N LEU B 216 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 219 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 222 through 230 removed outlier: 6.990A pdb=" N VAL B 230 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.646A pdb=" N SER B 240 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ILE C 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 251 through 253 removed outlier: 6.458A pdb=" N ASP B 252 " --> pdb=" O CYS A 253 " (cutoff:3.500A) 41 hydrogen bonds defined for protein. 123 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: 0.70 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1026 1.34 - 1.45: 538 1.45 - 1.57: 1712 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CA VAL B 230 " pdb=" C VAL B 230 " ideal model delta sigma weight residual 1.527 1.513 0.014 8.50e-03 1.38e+04 2.73e+00 bond pdb=" CA ARG B 247 " pdb=" C ARG B 247 " ideal model delta sigma weight residual 1.531 1.514 0.017 1.08e-02 8.57e+03 2.46e+00 bond pdb=" CA ARG A 247 " pdb=" C ARG A 247 " ideal model delta sigma weight residual 1.531 1.515 0.017 1.08e-02 8.57e+03 2.34e+00 bond pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 1.527 1.514 0.013 8.50e-03 1.38e+04 2.34e+00 bond pdb=" CA ARG C 247 " pdb=" C ARG C 247 " ideal model delta sigma weight residual 1.531 1.515 0.016 1.08e-02 8.57e+03 2.33e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 99.24 - 105.65: 34 105.65 - 112.06: 1695 112.06 - 118.48: 923 118.48 - 124.89: 1833 124.89 - 131.30: 18 Bond angle restraints: 4503 Sorted by residual: angle pdb=" C GLN C 245 " pdb=" N GLU C 246 " pdb=" CA GLU C 246 " ideal model delta sigma weight residual 122.11 117.17 4.94 1.59e+00 3.96e-01 9.66e+00 angle pdb=" C GLN B 245 " pdb=" N GLU B 246 " pdb=" CA GLU B 246 " ideal model delta sigma weight residual 122.11 117.17 4.94 1.59e+00 3.96e-01 9.66e+00 angle pdb=" C GLN A 245 " pdb=" N GLU A 246 " pdb=" CA GLU A 246 " ideal model delta sigma weight residual 122.11 117.21 4.90 1.59e+00 3.96e-01 9.50e+00 angle pdb=" C LEU A 144 " pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta sigma weight residual 121.54 126.70 -5.16 1.91e+00 2.74e-01 7.28e+00 angle pdb=" CA TYR C 143 " pdb=" CB TYR C 143 " pdb=" CG TYR C 143 " ideal model delta sigma weight residual 113.90 118.75 -4.85 1.80e+00 3.09e-01 7.27e+00 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 1794 16.36 - 32.72: 175 32.72 - 49.08: 17 49.08 - 65.43: 6 65.43 - 81.79: 3 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" CA GLN C 138 " pdb=" C GLN C 138 " pdb=" N LYS C 139 " pdb=" CA LYS C 139 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN A 138 " pdb=" C GLN A 138 " pdb=" N LYS A 139 " pdb=" CA LYS A 139 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLN B 138 " pdb=" C GLN B 138 " pdb=" N LYS B 139 " pdb=" CA LYS B 139 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 255 0.035 - 0.071: 156 0.071 - 0.106: 88 0.106 - 0.142: 35 0.142 - 0.177: 9 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ASN A 145 " pdb=" N ASN A 145 " pdb=" C ASN A 145 " pdb=" CB ASN A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA ASN C 145 " pdb=" N ASN C 145 " pdb=" C ASN C 145 " pdb=" CB ASN C 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA ASN B 145 " pdb=" N ASN B 145 " pdb=" C ASN B 145 " pdb=" CB ASN B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.018 2.00e-02 2.50e+03 1.14e-02 2.60e+00 pdb=" CG TYR A 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.018 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR C 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.018 2.00e-02 2.50e+03 1.12e-02 2.51e+00 pdb=" CG TYR B 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 385 2.75 - 3.29: 3104 3.29 - 3.83: 5256 3.83 - 4.36: 5810 4.36 - 4.90: 11622 Nonbonded interactions: 26177 Sorted by model distance: nonbonded pdb=" OH TYR B 236 " pdb=" OG SER B 240 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR A 236 " pdb=" OG SER A 240 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR C 236 " pdb=" OG SER C 240 " model vdw 2.218 2.440 nonbonded pdb=" OE2 GLU B 246 " pdb=" NH2 ARG B 247 " model vdw 2.300 2.520 nonbonded pdb=" OE2 GLU A 246 " pdb=" NH2 ARG A 247 " model vdw 2.300 2.520 ... (remaining 26172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 9.160 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.170 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.009 0.058 3312 Z= 0.583 Angle : 0.825 5.155 4503 Z= 0.494 Chirality : 0.060 0.177 543 Planarity : 0.003 0.011 558 Dihedral : 13.347 81.792 1206 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % 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: -5.71 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 222 PHE 0.010 0.003 PHE A 213 TYR 0.026 0.003 TYR A 143 ARG 0.003 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.381 Fit side-chains REVERT: B 140 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7233 (ttm110) REVERT: B 178 LYS cc_start: 0.7339 (mttt) cc_final: 0.6399 (tptt) REVERT: B 215 THR cc_start: 0.7671 (t) cc_final: 0.7398 (t) REVERT: A 140 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7490 (ttm110) REVERT: A 178 LYS cc_start: 0.7850 (mttt) cc_final: 0.6991 (tptt) REVERT: C 140 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7510 (ttm110) REVERT: C 178 LYS cc_start: 0.7310 (mttt) cc_final: 0.6486 (tptt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2524 time to fit residues: 14.5283 Evaluate side-chains 37 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 0.0170 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 0.0270 overall best weight: 2.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 156 ASN B 223 ASN A 156 ASN A 223 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 223 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3312 Z= 0.227 Angle : 0.586 5.540 4503 Z= 0.324 Chirality : 0.053 0.180 543 Planarity : 0.002 0.007 558 Dihedral : 6.479 19.318 447 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 3.44 % Allowed : 12.17 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.43 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.009 0.002 PHE A 237 TYR 0.017 0.002 TYR B 143 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.358 Fit side-chains REVERT: B 140 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7345 (ttm110) REVERT: B 145 ASN cc_start: 0.7399 (p0) cc_final: 0.7177 (p0) REVERT: B 146 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (pt) REVERT: B 178 LYS cc_start: 0.7297 (mttt) cc_final: 0.6486 (tptt) REVERT: B 215 THR cc_start: 0.7506 (t) cc_final: 0.7228 (t) REVERT: A 140 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7645 (ttm110) REVERT: A 146 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8228 (pt) REVERT: A 178 LYS cc_start: 0.7675 (mttt) cc_final: 0.6957 (tptt) REVERT: A 213 PHE cc_start: 0.8058 (t80) cc_final: 0.7803 (t80) REVERT: C 140 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7610 (ttm110) REVERT: C 145 ASN cc_start: 0.7721 (p0) cc_final: 0.7266 (p0) REVERT: C 146 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8005 (pt) REVERT: C 178 LYS cc_start: 0.7277 (mttt) cc_final: 0.6560 (tptt) REVERT: C 215 THR cc_start: 0.7732 (t) cc_final: 0.7500 (t) outliers start: 13 outliers final: 5 residues processed: 52 average time/residue: 0.1712 time to fit residues: 10.7739 Evaluate side-chains 49 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3312 Z= 0.276 Angle : 0.601 5.765 4503 Z= 0.333 Chirality : 0.053 0.178 543 Planarity : 0.002 0.008 558 Dihedral : 6.285 16.892 447 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 3.44 % Allowed : 13.76 % Favored : 82.80 % 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: -5.37 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 239 PHE 0.010 0.002 PHE A 237 TYR 0.019 0.002 TYR B 143 ARG 0.001 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.433 Fit side-chains REVERT: B 140 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7471 (ttm110) REVERT: B 145 ASN cc_start: 0.7367 (p0) cc_final: 0.6906 (p0) REVERT: B 146 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8238 (pt) REVERT: B 178 LYS cc_start: 0.7424 (mttt) cc_final: 0.6560 (tptt) REVERT: B 209 TYR cc_start: 0.7022 (m-80) cc_final: 0.6336 (m-80) REVERT: B 215 THR cc_start: 0.7580 (t) cc_final: 0.7256 (t) REVERT: A 140 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7664 (ttm110) REVERT: A 178 LYS cc_start: 0.7632 (mttt) cc_final: 0.6929 (tptt) REVERT: A 213 PHE cc_start: 0.8112 (t80) cc_final: 0.7787 (t80) REVERT: A 226 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7432 (tt) REVERT: C 145 ASN cc_start: 0.7723 (p0) cc_final: 0.7297 (p0) REVERT: C 146 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8021 (pt) REVERT: C 170 GLN cc_start: 0.8454 (mp10) cc_final: 0.8153 (mp10) REVERT: C 178 LYS cc_start: 0.7257 (mttt) cc_final: 0.6513 (tptt) outliers start: 13 outliers final: 8 residues processed: 60 average time/residue: 0.1725 time to fit residues: 12.5164 Evaluate side-chains 52 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3312 Z= 0.396 Angle : 0.660 5.330 4503 Z= 0.367 Chirality : 0.056 0.198 543 Planarity : 0.002 0.010 558 Dihedral : 6.523 18.380 447 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 5.82 % Allowed : 12.70 % Favored : 81.48 % 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: -5.42 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.012 0.002 PHE A 237 TYR 0.024 0.002 TYR B 143 ARG 0.005 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 0.321 Fit side-chains REVERT: B 140 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7485 (ttm110) REVERT: B 141 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8787 (t) REVERT: B 145 ASN cc_start: 0.7339 (p0) cc_final: 0.7082 (p0) REVERT: B 178 LYS cc_start: 0.7538 (mttt) cc_final: 0.6628 (tptt) REVERT: B 209 TYR cc_start: 0.6951 (m-80) cc_final: 0.6373 (m-80) REVERT: B 215 THR cc_start: 0.7755 (t) cc_final: 0.7407 (t) REVERT: B 226 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7649 (tt) REVERT: A 140 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7621 (ttm110) REVERT: A 178 LYS cc_start: 0.7683 (mttt) cc_final: 0.6902 (tptt) REVERT: A 226 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7471 (tt) REVERT: C 145 ASN cc_start: 0.7805 (p0) cc_final: 0.7359 (p0) REVERT: C 178 LYS cc_start: 0.7206 (mttt) cc_final: 0.6410 (tptt) REVERT: C 209 TYR cc_start: 0.7362 (m-80) cc_final: 0.6986 (m-80) outliers start: 22 outliers final: 16 residues processed: 65 average time/residue: 0.1501 time to fit residues: 12.0808 Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 3312 Z= 0.502 Angle : 0.712 5.946 4503 Z= 0.400 Chirality : 0.058 0.196 543 Planarity : 0.003 0.012 558 Dihedral : 6.772 20.403 447 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Rotamer: Outliers : 6.08 % Allowed : 13.23 % Favored : 80.69 % 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: -5.55 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 222 PHE 0.014 0.003 PHE A 237 TYR 0.027 0.003 TYR B 143 ARG 0.003 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 39 time to evaluate : 0.338 Fit side-chains REVERT: B 140 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7428 (ttm110) REVERT: B 141 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8707 (t) REVERT: B 145 ASN cc_start: 0.7384 (p0) cc_final: 0.6991 (p0) REVERT: B 178 LYS cc_start: 0.7520 (mttt) cc_final: 0.6581 (tptt) REVERT: B 215 THR cc_start: 0.8069 (t) cc_final: 0.7715 (t) REVERT: B 226 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 140 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7644 (ttm110) REVERT: A 178 LYS cc_start: 0.7692 (mttt) cc_final: 0.6881 (tptt) REVERT: C 145 ASN cc_start: 0.7772 (p0) cc_final: 0.7337 (p0) REVERT: C 178 LYS cc_start: 0.7224 (mttt) cc_final: 0.6385 (tptt) REVERT: C 207 MET cc_start: 0.7265 (ttm) cc_final: 0.6891 (ttt) REVERT: C 209 TYR cc_start: 0.7302 (m-80) cc_final: 0.7028 (m-80) outliers start: 23 outliers final: 18 residues processed: 61 average time/residue: 0.1489 time to fit residues: 11.1914 Evaluate side-chains 57 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 37 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 27 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 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3312 Z= 0.211 Angle : 0.573 5.412 4503 Z= 0.317 Chirality : 0.053 0.195 543 Planarity : 0.002 0.009 558 Dihedral : 6.095 16.623 447 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.82 % Allowed : 15.08 % Favored : 79.10 % 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: -5.26 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.006 0.001 PHE A 237 TYR 0.018 0.001 TYR B 143 ARG 0.003 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.382 Fit side-chains REVERT: B 140 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7463 (ttm110) REVERT: B 141 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8739 (t) REVERT: B 145 ASN cc_start: 0.7434 (p0) cc_final: 0.7198 (p0) REVERT: B 146 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8185 (pt) REVERT: B 178 LYS cc_start: 0.7419 (mttt) cc_final: 0.6546 (tptt) REVERT: B 215 THR cc_start: 0.7832 (t) cc_final: 0.7452 (t) REVERT: A 138 GLN cc_start: 0.8655 (pt0) cc_final: 0.8201 (pt0) REVERT: A 140 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7626 (ttm110) REVERT: A 178 LYS cc_start: 0.7646 (mttt) cc_final: 0.6919 (tptt) REVERT: C 145 ASN cc_start: 0.7843 (p0) cc_final: 0.7338 (p0) REVERT: C 146 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8047 (pt) REVERT: C 178 LYS cc_start: 0.7238 (mttt) cc_final: 0.6496 (tptt) REVERT: C 207 MET cc_start: 0.7305 (ttm) cc_final: 0.7037 (ttt) outliers start: 22 outliers final: 15 residues processed: 63 average time/residue: 0.1614 time to fit residues: 12.4464 Evaluate side-chains 58 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3312 Z= 0.181 Angle : 0.561 5.820 4503 Z= 0.307 Chirality : 0.052 0.181 543 Planarity : 0.002 0.008 558 Dihedral : 5.728 15.436 447 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 5.29 % Allowed : 14.81 % Favored : 79.89 % 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: -5.12 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.006 0.001 PHE A 237 TYR 0.015 0.001 TYR B 143 ARG 0.003 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.379 Fit side-chains REVERT: B 140 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7484 (ttm110) REVERT: B 145 ASN cc_start: 0.7479 (p0) cc_final: 0.7165 (p0) REVERT: B 146 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8155 (pt) REVERT: B 178 LYS cc_start: 0.7293 (mttt) cc_final: 0.6536 (tptt) REVERT: B 215 THR cc_start: 0.7638 (t) cc_final: 0.7260 (t) REVERT: A 140 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7649 (ttm110) REVERT: A 178 LYS cc_start: 0.7573 (mttt) cc_final: 0.6852 (tptt) REVERT: C 145 ASN cc_start: 0.7966 (p0) cc_final: 0.7432 (p0) REVERT: C 146 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8075 (pt) REVERT: C 178 LYS cc_start: 0.7204 (mttt) cc_final: 0.6469 (tptt) REVERT: C 207 MET cc_start: 0.7310 (ttm) cc_final: 0.7047 (ttt) outliers start: 20 outliers final: 13 residues processed: 64 average time/residue: 0.1562 time to fit residues: 12.2214 Evaluate side-chains 58 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 0.0870 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3312 Z= 0.254 Angle : 0.596 6.315 4503 Z= 0.328 Chirality : 0.053 0.188 543 Planarity : 0.002 0.010 558 Dihedral : 5.890 16.508 447 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 4.76 % Allowed : 16.40 % Favored : 78.84 % 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: -5.08 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.009 0.001 PHE B 237 TYR 0.018 0.002 TYR B 143 ARG 0.003 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.393 Fit side-chains REVERT: B 145 ASN cc_start: 0.7410 (p0) cc_final: 0.7182 (p0) REVERT: B 146 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8194 (pt) REVERT: B 178 LYS cc_start: 0.7350 (mttt) cc_final: 0.6499 (tptt) REVERT: B 209 TYR cc_start: 0.6879 (m-80) cc_final: 0.6584 (m-80) REVERT: A 178 LYS cc_start: 0.7655 (mttt) cc_final: 0.6851 (tptt) REVERT: C 145 ASN cc_start: 0.7850 (p0) cc_final: 0.7354 (p0) REVERT: C 146 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8069 (pt) REVERT: C 178 LYS cc_start: 0.7267 (mttt) cc_final: 0.6463 (tptt) REVERT: C 207 MET cc_start: 0.7354 (ttm) cc_final: 0.7068 (ttt) outliers start: 18 outliers final: 13 residues processed: 65 average time/residue: 0.1592 time to fit residues: 12.6689 Evaluate side-chains 61 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 3312 Z= 0.367 Angle : 0.668 6.588 4503 Z= 0.368 Chirality : 0.056 0.197 543 Planarity : 0.004 0.055 558 Dihedral : 6.289 18.695 447 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 4.50 % Allowed : 17.20 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.010 0.002 PHE B 237 TYR 0.022 0.002 TYR A 143 ARG 0.013 0.002 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.398 Fit side-chains REVERT: B 146 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8331 (pt) REVERT: B 178 LYS cc_start: 0.7433 (mttt) cc_final: 0.6575 (tptt) REVERT: B 215 THR cc_start: 0.8004 (t) cc_final: 0.7618 (t) REVERT: A 178 LYS cc_start: 0.7701 (mttt) cc_final: 0.6890 (tptt) REVERT: C 178 LYS cc_start: 0.7253 (mttt) cc_final: 0.6420 (tptt) REVERT: C 207 MET cc_start: 0.7398 (ttm) cc_final: 0.7099 (ttt) outliers start: 17 outliers final: 16 residues processed: 56 average time/residue: 0.1280 time to fit residues: 9.1863 Evaluate side-chains 56 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3312 Z= 0.264 Angle : 0.633 5.778 4503 Z= 0.347 Chirality : 0.055 0.255 543 Planarity : 0.004 0.048 558 Dihedral : 6.113 17.323 447 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 4.76 % Allowed : 17.46 % Favored : 77.78 % 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: -5.03 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.007 0.001 PHE B 237 TYR 0.020 0.002 TYR A 143 ARG 0.012 0.002 ARG B 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.391 Fit side-chains REVERT: B 145 ASN cc_start: 0.7572 (p0) cc_final: 0.7293 (p0) REVERT: B 146 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8169 (pt) REVERT: B 178 LYS cc_start: 0.7422 (mttt) cc_final: 0.6526 (tptt) REVERT: B 215 THR cc_start: 0.7849 (t) cc_final: 0.7464 (t) REVERT: A 178 LYS cc_start: 0.7712 (mttt) cc_final: 0.6849 (tptt) REVERT: C 145 ASN cc_start: 0.7000 (p0) cc_final: 0.6488 (t0) REVERT: C 146 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8076 (pt) REVERT: C 178 LYS cc_start: 0.7217 (mttt) cc_final: 0.6446 (tptt) REVERT: C 207 MET cc_start: 0.7337 (ttm) cc_final: 0.7057 (ttt) outliers start: 18 outliers final: 15 residues processed: 53 average time/residue: 0.1297 time to fit residues: 8.8440 Evaluate side-chains 54 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 37 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.0170 chunk 15 optimal weight: 3.9990 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.271397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.225061 restraints weight = 4059.776| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 0.85 r_work: 0.4887 rms_B_bonded: 0.50 restraints_weight: 0.5000 r_work: 0.4871 rms_B_bonded: 0.74 restraints_weight: 0.2500 r_work: 0.4750 rms_B_bonded: 2.46 restraints_weight: 0.1250 r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3312 Z= 0.235 Angle : 0.611 5.593 4503 Z= 0.334 Chirality : 0.054 0.233 543 Planarity : 0.003 0.046 558 Dihedral : 5.949 16.927 447 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 4.50 % Allowed : 17.72 % Favored : 77.78 % 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: -4.98 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.007 0.001 PHE B 237 TYR 0.018 0.002 TYR A 143 ARG 0.012 0.002 ARG A 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1223.05 seconds wall clock time: 23 minutes 9.02 seconds (1389.02 seconds total)