Starting phenix.real_space_refine on Fri Jul 19 03:36:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qg0_18386/07_2024/8qg0_18386.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qg0_18386/07_2024/8qg0_18386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qg0_18386/07_2024/8qg0_18386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qg0_18386/07_2024/8qg0_18386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qg0_18386/07_2024/8qg0_18386.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qg0_18386/07_2024/8qg0_18386.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 13 5.16 5 C 3811 2.51 5 N 1012 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6080 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3478 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain: "B" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNA': 17} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 15} Time building chain proxies: 4.54, per 1000 atoms: 0.75 Number of scatterers: 6080 At special positions: 0 Unit cell: (67.1, 91.3, 104.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 33 15.00 O 1211 8.00 N 1012 7.00 C 3811 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 - 3.50 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: 3.14 Conformation dependent library (CDL) restraints added in 999.0 milliseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 33.5% alpha, 13.7% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.583A pdb=" N ASN A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.972A pdb=" N TYR A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.808A pdb=" N ASN A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.948A pdb=" N ASN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.534A pdb=" N VAL A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 359 through 376 removed outlier: 3.516A pdb=" N HIS A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.660A pdb=" N GLN A 421 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 4.078A pdb=" N GLY B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.829A pdb=" N VAL B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 216 removed outlier: 3.531A pdb=" N PHE B 205 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 removed outlier: 6.841A pdb=" N ILE A 183 " --> pdb=" O HIS A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.557A pdb=" N CYS A 197 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 195 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.874A pdb=" N GLU A 212 " --> pdb=" O MET A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 293 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.608A pdb=" N ARG B 110 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.705A pdb=" N ASN B 30 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 234 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 223 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.716A pdb=" N SER B 38 " --> pdb=" O LEU B 61 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1447 1.33 - 1.45: 1410 1.45 - 1.57: 3348 1.57 - 1.69: 65 1.69 - 1.80: 25 Bond restraints: 6295 Sorted by residual: bond pdb=" N LEU A 249 " pdb=" CA LEU A 249 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.52e-02 4.33e+03 9.71e+00 bond pdb=" N ARG A 383 " pdb=" CA ARG A 383 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.21e-02 6.83e+03 9.59e+00 bond pdb=" N SER B 163 " pdb=" CA SER B 163 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.43e+00 bond pdb=" N ILE B 167 " pdb=" CA ILE B 167 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.26e+00 bond pdb=" N SER A 384 " pdb=" CA SER A 384 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 7.84e+00 ... (remaining 6290 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.96: 305 105.96 - 112.98: 3405 112.98 - 120.00: 2181 120.00 - 127.02: 2651 127.02 - 134.04: 142 Bond angle restraints: 8684 Sorted by residual: angle pdb=" C LYS B 168 " pdb=" CA LYS B 168 " pdb=" CB LYS B 168 " ideal model delta sigma weight residual 116.54 110.28 6.26 1.15e+00 7.56e-01 2.97e+01 angle pdb=" N LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta sigma weight residual 111.65 104.47 7.18 1.40e+00 5.10e-01 2.63e+01 angle pdb=" N LEU A 249 " pdb=" CA LEU A 249 " pdb=" C LEU A 249 " ideal model delta sigma weight residual 110.61 105.67 4.94 1.25e+00 6.40e-01 1.56e+01 angle pdb=" CA ILE B 167 " pdb=" C ILE B 167 " pdb=" O ILE B 167 " ideal model delta sigma weight residual 121.05 116.93 4.12 1.11e+00 8.12e-01 1.38e+01 angle pdb=" N TYR B 171 " pdb=" CA TYR B 171 " pdb=" C TYR B 171 " ideal model delta sigma weight residual 113.38 109.05 4.33 1.17e+00 7.31e-01 1.37e+01 ... (remaining 8679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3219 17.93 - 35.85: 360 35.85 - 53.78: 108 53.78 - 71.70: 38 71.70 - 89.63: 12 Dihedral angle restraints: 3737 sinusoidal: 1807 harmonic: 1930 Sorted by residual: dihedral pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta harmonic sigma weight residual 122.80 111.66 11.14 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" CA VAL A 300 " pdb=" C VAL A 300 " pdb=" N MET A 301 " pdb=" CA MET A 301 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TYR B 22 " pdb=" C TYR B 22 " pdb=" N ILE B 23 " pdb=" CA ILE B 23 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 930 0.103 - 0.205: 40 0.205 - 0.308: 1 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 972 Sorted by residual: chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CB ILE B 167 " pdb=" CA ILE B 167 " pdb=" CG1 ILE B 167 " pdb=" CG2 ILE B 167 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR B 164 " pdb=" N TYR B 164 " pdb=" C TYR B 164 " pdb=" CB TYR B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 969 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 40 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 41 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 355 " 0.011 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP A 355 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 355 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 355 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 355 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 355 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 355 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 355 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 355 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 355 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 341 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 342 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " 0.021 5.00e-02 4.00e+02 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 543 2.74 - 3.28: 6374 3.28 - 3.82: 10696 3.82 - 4.36: 13200 4.36 - 4.90: 21656 Nonbonded interactions: 52469 Sorted by model distance: nonbonded pdb=" O6 DG P 11 " pdb=" N6 A Q 6 " model vdw 2.198 2.520 nonbonded pdb=" NE ARG A 257 " pdb=" O2' A Q 15 " model vdw 2.208 2.520 nonbonded pdb=" O2 DC P 8 " pdb=" N2 G Q 11 " model vdw 2.220 2.520 nonbonded pdb=" OG1 THR A 250 " pdb=" O ALA A 288 " model vdw 2.239 2.440 nonbonded pdb=" O ILE A 87 " pdb=" NE2 GLN A 99 " model vdw 2.246 2.520 ... (remaining 52464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 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 : 0.004 0.052 6295 Z= 0.270 Angle : 0.728 9.538 8684 Z= 0.439 Chirality : 0.049 0.514 972 Planarity : 0.005 0.079 974 Dihedral : 17.660 89.630 2501 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.50 % Allowed : 0.50 % Favored : 99.00 % Cbeta Deviations : 0.32 % 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: -1.84 (0.33), residues: 652 helix: 0.39 (0.39), residues: 179 sheet: -2.31 (0.46), residues: 132 loop : -1.62 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 355 HIS 0.004 0.001 HIS A 291 PHE 0.018 0.002 PHE A 382 TYR 0.014 0.002 TYR A 323 ARG 0.007 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.645 Fit side-chains REVERT: B 21 LEU cc_start: 0.7830 (mp) cc_final: 0.7626 (mp) outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.1725 time to fit residues: 26.7243 Evaluate side-chains 99 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6295 Z= 0.264 Angle : 0.653 8.934 8684 Z= 0.343 Chirality : 0.047 0.204 972 Planarity : 0.005 0.059 974 Dihedral : 18.022 92.496 1155 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.65 % Allowed : 10.12 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.33), residues: 652 helix: 0.26 (0.38), residues: 196 sheet: -2.25 (0.44), residues: 138 loop : -1.89 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 355 HIS 0.004 0.001 HIS A 365 PHE 0.011 0.001 PHE B 205 TYR 0.012 0.001 TYR A 287 ARG 0.003 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.600 Fit side-chains REVERT: B 110 ARG cc_start: 0.5746 (mmm160) cc_final: 0.5290 (mmm160) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 0.1616 time to fit residues: 23.6665 Evaluate side-chains 106 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 199 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 354 ASN B 187 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6295 Z= 0.217 Angle : 0.612 9.563 8684 Z= 0.318 Chirality : 0.045 0.189 972 Planarity : 0.004 0.060 974 Dihedral : 17.977 93.118 1155 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.65 % Allowed : 13.27 % Favored : 83.08 % 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: -1.79 (0.33), residues: 652 helix: 0.33 (0.38), residues: 196 sheet: -2.06 (0.48), residues: 131 loop : -1.75 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS A 365 PHE 0.011 0.001 PHE B 205 TYR 0.009 0.001 TYR B 64 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.705 Fit side-chains REVERT: A 355 TRP cc_start: 0.7196 (m-10) cc_final: 0.6735 (m-10) REVERT: B 170 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6275 (tttt) REVERT: B 187 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6072 (t-170) outliers start: 22 outliers final: 16 residues processed: 106 average time/residue: 0.1676 time to fit residues: 24.1299 Evaluate side-chains 108 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.0370 chunk 17 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6295 Z= 0.251 Angle : 0.622 8.361 8684 Z= 0.326 Chirality : 0.046 0.180 972 Planarity : 0.005 0.079 974 Dihedral : 18.062 95.271 1155 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.65 % Allowed : 15.92 % Favored : 80.43 % 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: -1.86 (0.33), residues: 652 helix: 0.20 (0.38), residues: 200 sheet: -1.96 (0.48), residues: 129 loop : -1.84 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.006 0.001 HIS B 187 PHE 0.009 0.001 PHE A 426 TYR 0.016 0.002 TYR A 323 ARG 0.005 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.651 Fit side-chains REVERT: A 112 MET cc_start: 0.6515 (mtp) cc_final: 0.6280 (mtm) REVERT: A 355 TRP cc_start: 0.7191 (m-10) cc_final: 0.6595 (m-10) REVERT: B 187 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6036 (t70) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 0.1614 time to fit residues: 23.7812 Evaluate side-chains 112 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 199 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6295 Z= 0.288 Angle : 0.651 11.105 8684 Z= 0.339 Chirality : 0.046 0.172 972 Planarity : 0.005 0.066 974 Dihedral : 18.160 97.762 1155 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.98 % Allowed : 15.59 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.33), residues: 652 helix: 0.41 (0.38), residues: 187 sheet: -2.00 (0.48), residues: 129 loop : -1.79 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 76 HIS 0.003 0.001 HIS A 365 PHE 0.009 0.001 PHE A 298 TYR 0.013 0.002 TYR A 360 ARG 0.005 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.664 Fit side-chains REVERT: B 145 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6362 (tt) REVERT: B 187 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6637 (m-70) outliers start: 30 outliers final: 23 residues processed: 107 average time/residue: 0.1688 time to fit residues: 24.3643 Evaluate side-chains 114 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 199 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6295 Z= 0.195 Angle : 0.607 9.632 8684 Z= 0.314 Chirality : 0.045 0.218 972 Planarity : 0.005 0.059 974 Dihedral : 18.121 96.821 1155 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.98 % Allowed : 17.41 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.33), residues: 652 helix: 0.41 (0.38), residues: 196 sheet: -1.98 (0.48), residues: 129 loop : -1.73 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 76 HIS 0.004 0.001 HIS A 291 PHE 0.009 0.001 PHE A 426 TYR 0.013 0.001 TYR B 31 ARG 0.005 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.655 Fit side-chains REVERT: A 355 TRP cc_start: 0.7148 (m-10) cc_final: 0.6536 (m-10) REVERT: B 145 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6246 (tt) outliers start: 24 outliers final: 20 residues processed: 106 average time/residue: 0.1714 time to fit residues: 24.4559 Evaluate side-chains 111 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN B 187 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6295 Z= 0.219 Angle : 0.616 11.114 8684 Z= 0.318 Chirality : 0.045 0.174 972 Planarity : 0.005 0.057 974 Dihedral : 18.173 97.204 1155 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.31 % Allowed : 17.41 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.33), residues: 652 helix: 0.48 (0.38), residues: 195 sheet: -2.02 (0.48), residues: 129 loop : -1.67 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 76 HIS 0.005 0.001 HIS B 187 PHE 0.009 0.001 PHE A 426 TYR 0.010 0.001 TYR B 31 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.648 Fit side-chains REVERT: A 355 TRP cc_start: 0.7198 (m-10) cc_final: 0.6605 (m-10) REVERT: B 145 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6250 (tt) outliers start: 26 outliers final: 22 residues processed: 114 average time/residue: 0.1683 time to fit residues: 25.8250 Evaluate side-chains 116 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 199 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6295 Z= 0.231 Angle : 0.618 12.574 8684 Z= 0.320 Chirality : 0.044 0.157 972 Planarity : 0.005 0.058 974 Dihedral : 18.191 97.820 1155 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.48 % Allowed : 18.08 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.33), residues: 652 helix: 0.47 (0.38), residues: 195 sheet: -2.02 (0.48), residues: 129 loop : -1.70 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 76 HIS 0.004 0.001 HIS A 291 PHE 0.008 0.001 PHE A 426 TYR 0.010 0.001 TYR B 31 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.645 Fit side-chains REVERT: A 112 MET cc_start: 0.6026 (mtm) cc_final: 0.5619 (mtp) REVERT: B 145 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6210 (tt) outliers start: 27 outliers final: 22 residues processed: 109 average time/residue: 0.1623 time to fit residues: 23.9549 Evaluate side-chains 116 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 199 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6295 Z= 0.223 Angle : 0.627 13.478 8684 Z= 0.323 Chirality : 0.044 0.156 972 Planarity : 0.005 0.058 974 Dihedral : 18.195 97.718 1155 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.98 % Allowed : 18.91 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.33), residues: 652 helix: 0.58 (0.38), residues: 195 sheet: -2.02 (0.47), residues: 129 loop : -1.65 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 355 HIS 0.005 0.001 HIS B 187 PHE 0.008 0.001 PHE A 426 TYR 0.010 0.001 TYR B 31 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.658 Fit side-chains REVERT: A 112 MET cc_start: 0.6267 (mtm) cc_final: 0.6040 (mtp) REVERT: A 355 TRP cc_start: 0.7169 (m-10) cc_final: 0.6435 (m-10) REVERT: B 145 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6202 (tt) outliers start: 24 outliers final: 22 residues processed: 109 average time/residue: 0.1686 time to fit residues: 24.8179 Evaluate side-chains 116 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6295 Z= 0.219 Angle : 0.624 14.012 8684 Z= 0.321 Chirality : 0.044 0.153 972 Planarity : 0.005 0.058 974 Dihedral : 18.193 97.592 1155 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.81 % Allowed : 18.91 % Favored : 77.28 % 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: -1.56 (0.33), residues: 652 helix: 0.58 (0.38), residues: 195 sheet: -1.98 (0.48), residues: 129 loop : -1.62 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 76 HIS 0.004 0.001 HIS A 291 PHE 0.008 0.001 PHE A 426 TYR 0.011 0.001 TYR A 323 ARG 0.006 0.000 ARG B 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.664 Fit side-chains REVERT: A 355 TRP cc_start: 0.7161 (m-10) cc_final: 0.6412 (m-10) REVERT: B 145 ILE cc_start: 0.6494 (OUTLIER) cc_final: 0.6206 (tt) outliers start: 23 outliers final: 21 residues processed: 105 average time/residue: 0.1713 time to fit residues: 24.3137 Evaluate side-chains 115 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.214615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.194469 restraints weight = 7668.508| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 2.17 r_work: 0.4410 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6295 Z= 0.196 Angle : 0.610 13.969 8684 Z= 0.315 Chirality : 0.044 0.157 972 Planarity : 0.005 0.059 974 Dihedral : 18.167 96.998 1155 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.32 % Allowed : 19.90 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.34), residues: 652 helix: 0.65 (0.38), residues: 195 sheet: -1.98 (0.48), residues: 129 loop : -1.55 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 76 HIS 0.004 0.001 HIS A 291 PHE 0.008 0.001 PHE A 426 TYR 0.010 0.001 TYR A 323 ARG 0.006 0.001 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1551.69 seconds wall clock time: 28 minutes 21.45 seconds (1701.45 seconds total)