Starting phenix.real_space_refine on Fri Feb 16 15:17:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/02_2024/6wu2_21903_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/02_2024/6wu2_21903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/02_2024/6wu2_21903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/02_2024/6wu2_21903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/02_2024/6wu2_21903_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/02_2024/6wu2_21903_neut_trim_updated.pdb" } resolution = 3.36 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 S 50 5.16 5 C 5106 2.51 5 N 1176 2.21 5 O 1260 1.98 5 H 7812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 458": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15404 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 7666 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain: "B" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 7666 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'D10': 1, 'HEX': 3, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'D10': 1, 'HEX': 3, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.92, per 1000 atoms: 0.51 Number of scatterers: 15404 At special positions: 0 Unit cell: (78.8955, 102.723, 76.7775, 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 50 16.00 O 1260 8.00 N 1176 7.00 C 5106 6.00 H 7812 1.00 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: 14.85 Conformation dependent library (CDL) restraints added in 1.5 seconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 0 sheets defined 72.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 4.056A pdb=" N TRP A 14 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Proline residue: A 15 - end of helix Proline residue: A 27 - end of helix Processing helix chain 'A' and resid 35 through 53 Processing helix chain 'A' and resid 58 through 71 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 119 through 131 Processing helix chain 'A' and resid 135 through 151 removed outlier: 3.645A pdb=" N ALA A 151 " --> pdb=" O MET A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 229 through 254 removed outlier: 5.196A pdb=" N VAL A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 281 through 301 removed outlier: 3.959A pdb=" N GLY A 301 " --> pdb=" O TRP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.744A pdb=" N LEU A 345 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 357 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 377 through 390 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 399 through 416 removed outlier: 5.863A pdb=" N LEU A 407 " --> pdb=" O THR A 403 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 420 through 435 removed outlier: 5.174A pdb=" N ALA A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 456 through 485 Processing helix chain 'B' and resid 9 through 28 removed outlier: 4.057A pdb=" N TRP B 14 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Proline residue: B 15 - end of helix Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 35 through 53 Processing helix chain 'B' and resid 58 through 71 Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 119 through 131 Processing helix chain 'B' and resid 135 through 151 removed outlier: 3.644A pdb=" N ALA B 151 " --> pdb=" O MET B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 188 through 205 Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 229 through 254 removed outlier: 5.197A pdb=" N VAL B 238 " --> pdb=" O TRP B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Proline residue: B 248 - end of helix Processing helix chain 'B' and resid 265 through 275 Processing helix chain 'B' and resid 281 through 301 removed outlier: 3.957A pdb=" N GLY B 301 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 336 through 357 removed outlier: 3.744A pdb=" N LEU B 345 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 357 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 377 through 390 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 399 through 416 removed outlier: 5.864A pdb=" N LEU B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 420 through 435 removed outlier: 5.175A pdb=" N ALA B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 456 through 485 476 hydrogen bonds defined for protein. 1182 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: 5.44 Time building geometry restraints manager: 15.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7808 1.03 - 1.22: 4 1.22 - 1.42: 3156 1.42 - 1.61: 4544 1.61 - 1.81: 96 Bond restraints: 15608 Sorted by residual: bond pdb=" C SER B 177 " pdb=" N LYS B 178 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 8.92e+00 bond pdb=" C SER A 177 " pdb=" N LYS A 178 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 8.90e+00 bond pdb=" C3 D10 A 503 " pdb=" C4 D10 A 503 " ideal model delta sigma weight residual 1.523 1.484 0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" C6 D10 A 503 " pdb=" C7 D10 A 503 " ideal model delta sigma weight residual 1.524 1.490 0.034 2.00e-02 2.50e+03 2.90e+00 bond pdb=" C3 D10 B 503 " pdb=" C4 D10 B 503 " ideal model delta sigma weight residual 1.523 1.489 0.034 2.00e-02 2.50e+03 2.86e+00 ... (remaining 15603 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.69: 191 105.69 - 112.77: 18744 112.77 - 119.85: 3878 119.85 - 126.93: 5366 126.93 - 134.01: 155 Bond angle restraints: 28334 Sorted by residual: angle pdb=" C4 D10 A 503 " pdb=" C5 D10 A 503 " pdb=" C6 D10 A 503 " ideal model delta sigma weight residual 113.31 100.76 12.55 3.00e+00 1.11e-01 1.75e+01 angle pdb=" C4 D10 B 503 " pdb=" C5 D10 B 503 " pdb=" C6 D10 B 503 " ideal model delta sigma weight residual 113.31 102.22 11.09 3.00e+00 1.11e-01 1.37e+01 angle pdb=" N GLY A 398 " pdb=" CA GLY A 398 " pdb=" C GLY A 398 " ideal model delta sigma weight residual 114.67 109.62 5.05 1.41e+00 5.03e-01 1.28e+01 angle pdb=" N GLY B 398 " pdb=" CA GLY B 398 " pdb=" C GLY B 398 " ideal model delta sigma weight residual 114.67 109.65 5.02 1.41e+00 5.03e-01 1.27e+01 angle pdb=" C6 D10 A 503 " pdb=" C7 D10 A 503 " pdb=" C8 D10 A 503 " ideal model delta sigma weight residual 113.25 103.67 9.58 3.00e+00 1.11e-01 1.02e+01 ... (remaining 28329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 6301 17.43 - 34.86: 699 34.86 - 52.29: 232 52.29 - 69.72: 67 69.72 - 87.15: 17 Dihedral angle restraints: 7316 sinusoidal: 3890 harmonic: 3426 Sorted by residual: dihedral pdb=" CA LYS B 54 " pdb=" C LYS B 54 " pdb=" N PRO B 55 " pdb=" CA PRO B 55 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LYS A 54 " pdb=" C LYS A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PRO A 57 " pdb=" C PRO A 57 " pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta harmonic sigma weight residual -180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 557 0.027 - 0.053: 347 0.053 - 0.080: 242 0.080 - 0.106: 78 0.106 - 0.133: 18 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA ILE A 305 " pdb=" N ILE A 305 " pdb=" C ILE A 305 " pdb=" CB ILE A 305 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE B 305 " pdb=" N ILE B 305 " pdb=" C ILE B 305 " pdb=" CB ILE B 305 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 153 " pdb=" N ILE B 153 " pdb=" C ILE B 153 " pdb=" CB ILE B 153 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1239 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 475 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C GLY A 475 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A 475 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 476 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 475 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C GLY B 475 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY B 475 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE B 476 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 342 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C LEU B 342 " -0.025 2.00e-02 2.50e+03 pdb=" O LEU B 342 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE B 343 " 0.008 2.00e-02 2.50e+03 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 260 2.07 - 2.70: 25658 2.70 - 3.33: 46404 3.33 - 3.97: 57592 3.97 - 4.60: 93745 Nonbonded interactions: 223659 Sorted by model distance: nonbonded pdb=" O ARG A 134 " pdb=" H GLY A 137 " model vdw 1.431 1.850 nonbonded pdb=" O ARG B 134 " pdb=" H GLY B 137 " model vdw 1.431 1.850 nonbonded pdb=" O LEU A 387 " pdb=" HG1 THR A 391 " model vdw 1.562 1.850 nonbonded pdb=" O GLY B 443 " pdb=" HG SER B 446 " model vdw 1.585 1.850 nonbonded pdb=" O TRP A 234 " pdb=" HE1 TRP A 481 " model vdw 1.591 1.850 ... (remaining 223654 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' } 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: 12.160 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: 15.730 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 59.820 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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: 0.010 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: 91.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.010 0.062 7796 Z= 0.627 Angle : 0.767 12.550 10602 Z= 0.411 Chirality : 0.045 0.133 1242 Planarity : 0.004 0.031 1254 Dihedral : 14.776 72.458 2692 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.80 % Favored : 91.99 % Rotamer: Outliers : 0.76 % Allowed : 14.56 % Favored : 84.68 % 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: -3.14 (0.23), residues: 974 helix: -1.56 (0.16), residues: 754 sheet: None (None), residues: 0 loop : -3.36 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 344 HIS 0.005 0.001 HIS B 439 PHE 0.013 0.001 PHE B 360 TYR 0.011 0.001 TYR B 140 ARG 0.002 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 234 TRP cc_start: 0.6608 (t-100) cc_final: 0.6338 (t60) REVERT: A 356 ILE cc_start: 0.8895 (tt) cc_final: 0.8679 (mt) REVERT: A 369 GLN cc_start: 0.8509 (tt0) cc_final: 0.8143 (mt0) REVERT: B 103 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 234 TRP cc_start: 0.6634 (t-100) cc_final: 0.6340 (t60) REVERT: B 356 ILE cc_start: 0.8880 (tt) cc_final: 0.8667 (mt) REVERT: B 369 GLN cc_start: 0.8511 (tt0) cc_final: 0.8163 (mt0) outliers start: 6 outliers final: 4 residues processed: 119 average time/residue: 0.3654 time to fit residues: 62.6652 Evaluate side-chains 101 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 368 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 180 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN B 36 GLN B 180 ASN B 226 GLN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7796 Z= 0.168 Angle : 0.537 4.598 10602 Z= 0.294 Chirality : 0.039 0.153 1242 Planarity : 0.005 0.041 1254 Dihedral : 6.000 56.842 1066 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.44 % Favored : 94.35 % Rotamer: Outliers : 1.39 % Allowed : 14.56 % Favored : 84.05 % 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: -1.35 (0.25), residues: 974 helix: -0.34 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -2.49 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 344 HIS 0.003 0.001 HIS B 197 PHE 0.012 0.001 PHE A 474 TYR 0.013 0.001 TYR B 140 ARG 0.002 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 234 TRP cc_start: 0.6593 (t-100) cc_final: 0.6328 (t60) REVERT: A 264 ASN cc_start: 0.7265 (t0) cc_final: 0.6996 (t0) REVERT: A 331 ASP cc_start: 0.7936 (m-30) cc_final: 0.7493 (m-30) REVERT: A 369 GLN cc_start: 0.8529 (tt0) cc_final: 0.8189 (mt0) REVERT: B 234 TRP cc_start: 0.6644 (t-100) cc_final: 0.6370 (t60) REVERT: B 264 ASN cc_start: 0.7297 (t0) cc_final: 0.7043 (t0) REVERT: B 369 GLN cc_start: 0.8549 (tt0) cc_final: 0.8201 (mt0) outliers start: 11 outliers final: 6 residues processed: 126 average time/residue: 0.3119 time to fit residues: 61.2807 Evaluate side-chains 108 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7796 Z= 0.241 Angle : 0.540 4.641 10602 Z= 0.296 Chirality : 0.040 0.136 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.594 46.908 1064 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 1.65 % Allowed : 15.44 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 974 helix: 0.24 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -2.05 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 344 HIS 0.006 0.001 HIS A 112 PHE 0.012 0.001 PHE B 474 TYR 0.008 0.001 TYR B 140 ARG 0.001 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 234 TRP cc_start: 0.6779 (t-100) cc_final: 0.6463 (t60) REVERT: A 331 ASP cc_start: 0.8015 (m-30) cc_final: 0.7550 (m-30) REVERT: A 369 GLN cc_start: 0.8590 (tt0) cc_final: 0.8208 (mt0) REVERT: B 234 TRP cc_start: 0.6797 (t-100) cc_final: 0.6490 (t60) REVERT: B 331 ASP cc_start: 0.7943 (m-30) cc_final: 0.7482 (m-30) REVERT: B 369 GLN cc_start: 0.8586 (tt0) cc_final: 0.8222 (mt0) outliers start: 13 outliers final: 10 residues processed: 115 average time/residue: 0.3074 time to fit residues: 53.7483 Evaluate side-chains 110 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7796 Z= 0.234 Angle : 0.535 4.580 10602 Z= 0.290 Chirality : 0.040 0.146 1242 Planarity : 0.005 0.042 1254 Dihedral : 5.401 45.254 1062 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 1.52 % Allowed : 15.95 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.27), residues: 974 helix: 0.58 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.74 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.006 0.001 HIS B 112 PHE 0.011 0.001 PHE A 474 TYR 0.009 0.001 TYR B 140 ARG 0.001 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 234 TRP cc_start: 0.6850 (t-100) cc_final: 0.6494 (t60) REVERT: A 369 GLN cc_start: 0.8601 (tt0) cc_final: 0.8202 (mt0) REVERT: B 234 TRP cc_start: 0.6833 (t-100) cc_final: 0.6490 (t60) REVERT: B 331 ASP cc_start: 0.7952 (m-30) cc_final: 0.7491 (m-30) REVERT: B 369 GLN cc_start: 0.8602 (tt0) cc_final: 0.8220 (mt0) outliers start: 12 outliers final: 11 residues processed: 119 average time/residue: 0.2985 time to fit residues: 54.5728 Evaluate side-chains 108 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7796 Z= 0.216 Angle : 0.532 4.565 10602 Z= 0.288 Chirality : 0.039 0.165 1242 Planarity : 0.005 0.042 1254 Dihedral : 5.294 44.388 1062 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 2.03 % Allowed : 16.46 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 974 helix: 0.79 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.60 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 344 HIS 0.005 0.001 HIS B 197 PHE 0.009 0.001 PHE A 474 TYR 0.009 0.001 TYR A 140 ARG 0.001 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 TRP cc_start: 0.6879 (t-100) cc_final: 0.6485 (t60) REVERT: B 234 TRP cc_start: 0.6883 (t-100) cc_final: 0.6497 (t60) REVERT: B 331 ASP cc_start: 0.7973 (m-30) cc_final: 0.7509 (m-30) REVERT: B 369 GLN cc_start: 0.8618 (tt0) cc_final: 0.8242 (mt0) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.3253 time to fit residues: 61.0762 Evaluate side-chains 112 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7796 Z= 0.337 Angle : 0.597 5.055 10602 Z= 0.328 Chirality : 0.042 0.181 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.714 49.317 1062 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.78 % Favored : 93.02 % Rotamer: Outliers : 2.15 % Allowed : 16.96 % Favored : 80.89 % 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: 0.31 (0.28), residues: 974 helix: 0.73 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.49 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 344 HIS 0.005 0.001 HIS A 112 PHE 0.012 0.001 PHE A 474 TYR 0.011 0.001 TYR A 140 ARG 0.001 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8505 (t0) cc_final: 0.8168 (t0) REVERT: A 234 TRP cc_start: 0.6963 (t-100) cc_final: 0.6551 (t60) REVERT: B 176 ASP cc_start: 0.8484 (t0) cc_final: 0.8155 (t0) REVERT: B 234 TRP cc_start: 0.6973 (t-100) cc_final: 0.6555 (t60) REVERT: B 331 ASP cc_start: 0.7994 (m-30) cc_final: 0.7505 (m-30) outliers start: 17 outliers final: 16 residues processed: 133 average time/residue: 0.2815 time to fit residues: 57.6627 Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7796 Z= 0.162 Angle : 0.522 4.650 10602 Z= 0.281 Chirality : 0.039 0.166 1242 Planarity : 0.005 0.042 1254 Dihedral : 5.379 50.015 1062 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.75 % Favored : 94.05 % Rotamer: Outliers : 1.27 % Allowed : 18.73 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 974 helix: 0.90 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -1.29 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 344 HIS 0.008 0.001 HIS A 112 PHE 0.010 0.001 PHE A 474 TYR 0.007 0.001 TYR A 140 ARG 0.001 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8433 (t0) cc_final: 0.7996 (t0) REVERT: A 234 TRP cc_start: 0.6934 (t-100) cc_final: 0.6500 (t60) REVERT: B 176 ASP cc_start: 0.8414 (t0) cc_final: 0.8001 (t0) REVERT: B 234 TRP cc_start: 0.6944 (t-100) cc_final: 0.6512 (t60) REVERT: B 331 ASP cc_start: 0.8022 (m-30) cc_final: 0.7534 (m-30) outliers start: 10 outliers final: 10 residues processed: 124 average time/residue: 0.3002 time to fit residues: 57.3113 Evaluate side-chains 120 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7796 Z= 0.178 Angle : 0.518 4.548 10602 Z= 0.278 Chirality : 0.039 0.171 1242 Planarity : 0.005 0.041 1254 Dihedral : 5.182 52.219 1062 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.78 % Favored : 93.02 % Rotamer: Outliers : 1.90 % Allowed : 18.10 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 974 helix: 1.03 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 344 HIS 0.006 0.001 HIS A 112 PHE 0.010 0.001 PHE B 474 TYR 0.007 0.001 TYR A 140 ARG 0.001 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8419 (t0) cc_final: 0.7980 (t0) REVERT: A 234 TRP cc_start: 0.6933 (t-100) cc_final: 0.6469 (t60) REVERT: B 176 ASP cc_start: 0.8412 (t0) cc_final: 0.8000 (t0) REVERT: B 234 TRP cc_start: 0.6936 (t-100) cc_final: 0.6472 (t60) REVERT: B 331 ASP cc_start: 0.8009 (m-30) cc_final: 0.7510 (m-30) outliers start: 15 outliers final: 14 residues processed: 124 average time/residue: 0.2892 time to fit residues: 55.6421 Evaluate side-chains 124 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7796 Z= 0.251 Angle : 0.541 4.618 10602 Z= 0.293 Chirality : 0.040 0.203 1242 Planarity : 0.005 0.041 1254 Dihedral : 5.296 55.440 1062 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.29 % Favored : 92.51 % Rotamer: Outliers : 2.28 % Allowed : 18.23 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 974 helix: 0.95 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -1.57 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 344 HIS 0.006 0.001 HIS B 112 PHE 0.010 0.001 PHE A 474 TYR 0.008 0.001 TYR B 140 ARG 0.001 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8472 (t0) cc_final: 0.8050 (t0) REVERT: A 234 TRP cc_start: 0.6933 (t-100) cc_final: 0.6478 (t60) REVERT: B 176 ASP cc_start: 0.8458 (t0) cc_final: 0.8155 (t0) REVERT: B 234 TRP cc_start: 0.6942 (t-100) cc_final: 0.6482 (t60) REVERT: B 331 ASP cc_start: 0.8014 (m-30) cc_final: 0.7524 (m-30) outliers start: 18 outliers final: 16 residues processed: 130 average time/residue: 0.2930 time to fit residues: 58.8633 Evaluate side-chains 128 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7796 Z= 0.159 Angle : 0.509 4.509 10602 Z= 0.272 Chirality : 0.039 0.179 1242 Planarity : 0.005 0.041 1254 Dihedral : 5.174 59.393 1062 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.37 % Favored : 93.43 % Rotamer: Outliers : 1.90 % Allowed : 18.61 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.28), residues: 974 helix: 1.07 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.66 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 344 HIS 0.005 0.001 HIS A 112 PHE 0.009 0.001 PHE B 474 TYR 0.006 0.001 TYR A 140 ARG 0.001 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8415 (t0) cc_final: 0.7987 (t0) REVERT: A 234 TRP cc_start: 0.6925 (t-100) cc_final: 0.6448 (t60) REVERT: B 176 ASP cc_start: 0.8411 (t0) cc_final: 0.8010 (t0) REVERT: B 234 TRP cc_start: 0.6920 (t-100) cc_final: 0.6445 (t60) REVERT: B 331 ASP cc_start: 0.8007 (m-30) cc_final: 0.7505 (m-30) outliers start: 15 outliers final: 14 residues processed: 126 average time/residue: 0.2923 time to fit residues: 56.5342 Evaluate side-chains 124 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 432 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** 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 = 0.3684 r_free = 0.3684 target = 0.136337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125145 restraints weight = 32247.940| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.00 r_work: 0.3368 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7796 Z= 0.159 Angle : 0.506 4.491 10602 Z= 0.271 Chirality : 0.039 0.181 1242 Planarity : 0.005 0.041 1254 Dihedral : 5.059 55.137 1062 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.16 % Favored : 93.53 % Rotamer: Outliers : 1.52 % Allowed : 19.37 % Favored : 79.11 % 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: 0.81 (0.28), residues: 974 helix: 1.15 (0.19), residues: 770 sheet: None (None), residues: 0 loop : -1.71 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 344 HIS 0.006 0.001 HIS B 112 PHE 0.009 0.001 PHE B 474 TYR 0.006 0.001 TYR B 140 ARG 0.001 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3700.86 seconds wall clock time: 67 minutes 3.49 seconds (4023.49 seconds total)