Starting phenix.real_space_refine on Sat Jan 20 15:57:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/01_2024/6wu2_21903_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/01_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_21903/01_2024/6wu2_21903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/01_2024/6wu2_21903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/01_2024/6wu2_21903_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu2_21903/01_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-1.21-5211/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: 8.26, per 1000 atoms: 0.54 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: 16.27 Conformation dependent library (CDL) restraints added in 1.9 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: 2.86 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: 8.77 Time building geometry restraints manager: 15.80 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: 6279 17.43 - 34.86: 658 34.86 - 52.29: 153 52.29 - 69.72: 37 69.72 - 87.15: 17 Dihedral angle restraints: 7144 sinusoidal: 3718 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 7141 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: 6.470 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: 11.890 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 64.180 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.070 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.220 ------------------------------------------------------------------------------- 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 : 1.142 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: 0.3884 time to fit residues: 66.6290 Evaluate side-chains 101 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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: 0.5980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8332 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7796 Z= 0.178 Angle : 0.544 4.587 10602 Z= 0.300 Chirality : 0.039 0.159 1242 Planarity : 0.005 0.041 1254 Dihedral : 6.046 56.011 1066 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.44 % Favored : 94.35 % Rotamer: Outliers : 1.39 % Allowed : 14.81 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 974 helix: -0.38 (0.18), residues: 754 sheet: None (None), residues: 0 loop : -2.57 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.004 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 124 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 234 TRP cc_start: 0.6609 (t-100) cc_final: 0.6335 (t60) REVERT: A 331 ASP cc_start: 0.7936 (m-30) cc_final: 0.7533 (m-30) REVERT: A 369 GLN cc_start: 0.8529 (tt0) cc_final: 0.8187 (mt0) REVERT: B 234 TRP cc_start: 0.6654 (t-100) cc_final: 0.6371 (t60) REVERT: B 369 GLN cc_start: 0.8536 (tt0) cc_final: 0.8199 (mt0) outliers start: 11 outliers final: 6 residues processed: 121 average time/residue: 0.2995 time to fit residues: 55.8624 Evaluate side-chains 107 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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: 3.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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: 0.8393 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7796 Z= 0.211 Angle : 0.523 4.455 10602 Z= 0.285 Chirality : 0.039 0.133 1242 Planarity : 0.005 0.042 1254 Dihedral : 5.535 47.178 1064 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.16 % Favored : 93.63 % Rotamer: Outliers : 1.52 % Allowed : 15.44 % Favored : 83.04 % 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: -0.53 (0.26), residues: 974 helix: 0.21 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -2.08 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 344 HIS 0.004 0.001 HIS B 197 PHE 0.012 0.001 PHE A 474 TYR 0.008 0.001 TYR B 140 ARG 0.001 0.000 ARG B 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 119 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8140 (tt0) cc_final: 0.7885 (tt0) REVERT: A 234 TRP cc_start: 0.6728 (t-100) cc_final: 0.6430 (t60) REVERT: A 331 ASP cc_start: 0.8032 (m-30) cc_final: 0.7555 (m-30) REVERT: A 369 GLN cc_start: 0.8583 (tt0) cc_final: 0.8203 (mt0) REVERT: B 234 TRP cc_start: 0.6792 (t-100) cc_final: 0.6471 (t60) REVERT: B 331 ASP cc_start: 0.7942 (m-30) cc_final: 0.7479 (m-30) REVERT: B 369 GLN cc_start: 0.8583 (tt0) cc_final: 0.8226 (mt0) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.2973 time to fit residues: 51.5622 Evaluate side-chains 107 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7796 Z= 0.258 Angle : 0.554 4.641 10602 Z= 0.301 Chirality : 0.040 0.147 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.456 45.002 1062 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.47 % Favored : 93.33 % Rotamer: Outliers : 1.90 % Allowed : 16.46 % Favored : 81.65 % 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: 0.03 (0.27), residues: 974 helix: 0.56 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.74 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 344 HIS 0.007 0.001 HIS B 112 PHE 0.012 0.001 PHE A 474 TYR 0.009 0.001 TYR A 140 ARG 0.001 0.000 ARG A 122 *********************** 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 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 TRP cc_start: 0.6897 (t-100) cc_final: 0.6517 (t60) REVERT: A 331 ASP cc_start: 0.7980 (m-30) cc_final: 0.7535 (m-30) REVERT: B 234 TRP cc_start: 0.6889 (t-100) cc_final: 0.6524 (t60) REVERT: B 331 ASP cc_start: 0.7960 (m-30) cc_final: 0.7481 (m-30) REVERT: B 369 GLN cc_start: 0.8612 (tt0) cc_final: 0.8241 (mt0) outliers start: 15 outliers final: 13 residues processed: 125 average time/residue: 0.2983 time to fit residues: 57.0815 Evaluate side-chains 111 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2848 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= 0.241 Angle : 0.535 4.616 10602 Z= 0.290 Chirality : 0.040 0.153 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.357 44.005 1062 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.37 % Favored : 93.43 % Rotamer: Outliers : 1.90 % Allowed : 17.34 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.28), residues: 974 helix: 0.77 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.006 0.001 HIS A 112 PHE 0.011 0.001 PHE A 474 TYR 0.009 0.001 TYR A 140 ARG 0.001 0.000 ARG A 184 *********************** 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 125 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8395 (t0) cc_final: 0.7961 (t0) REVERT: A 234 TRP cc_start: 0.6901 (t-100) cc_final: 0.6509 (t60) REVERT: B 234 TRP cc_start: 0.6915 (t-100) cc_final: 0.6520 (t60) REVERT: B 331 ASP cc_start: 0.7997 (m-30) cc_final: 0.7520 (m-30) outliers start: 15 outliers final: 14 residues processed: 123 average time/residue: 0.2866 time to fit residues: 54.7971 Evaluate side-chains 116 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** B 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7796 Z= 0.380 Angle : 0.612 5.186 10602 Z= 0.336 Chirality : 0.043 0.175 1242 Planarity : 0.006 0.045 1254 Dihedral : 5.855 51.940 1062 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.29 % Favored : 92.51 % Rotamer: Outliers : 2.15 % Allowed : 18.10 % Favored : 79.75 % 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: 0.20 (0.28), residues: 974 helix: 0.67 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.57 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 344 HIS 0.005 0.001 HIS B 112 PHE 0.012 0.001 PHE A 474 TYR 0.012 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 139 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8542 (t0) cc_final: 0.8090 (t0) REVERT: A 234 TRP cc_start: 0.6984 (t-100) cc_final: 0.6577 (t60) REVERT: B 176 ASP cc_start: 0.8510 (t0) cc_final: 0.8097 (t0) REVERT: B 234 TRP cc_start: 0.6989 (t-100) cc_final: 0.6571 (t60) REVERT: B 331 ASP cc_start: 0.8015 (m-30) cc_final: 0.7534 (m-30) outliers start: 17 outliers final: 17 residues processed: 137 average time/residue: 0.2845 time to fit residues: 59.9250 Evaluate side-chains 129 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 123 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=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: 2.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7796 Z= 0.176 Angle : 0.525 4.561 10602 Z= 0.281 Chirality : 0.039 0.159 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.445 54.051 1062 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.74 % Rotamer: Outliers : 1.65 % Allowed : 19.37 % Favored : 78.99 % 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: 0.52 (0.28), residues: 974 helix: 0.86 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 344 HIS 0.008 0.001 HIS B 112 PHE 0.011 0.001 PHE B 474 TYR 0.008 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 132 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8474 (t0) cc_final: 0.8034 (t0) REVERT: A 234 TRP cc_start: 0.6946 (t-100) cc_final: 0.6517 (t60) REVERT: B 176 ASP cc_start: 0.8447 (t0) cc_final: 0.8130 (t0) REVERT: B 234 TRP cc_start: 0.6957 (t-100) cc_final: 0.6532 (t60) REVERT: B 331 ASP cc_start: 0.8025 (m-30) cc_final: 0.7547 (m-30) outliers start: 13 outliers final: 12 residues processed: 130 average time/residue: 0.2986 time to fit residues: 59.5869 Evaluate side-chains 126 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER 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 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 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: 3.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 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 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: 0.8519 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7796 Z= 0.289 Angle : 0.562 4.693 10602 Z= 0.306 Chirality : 0.041 0.190 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.524 58.006 1062 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.39 % Favored : 92.40 % Rotamer: Outliers : 2.03 % Allowed : 19.37 % 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: 0.50 (0.28), residues: 974 helix: 0.86 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.41 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.007 0.001 HIS B 112 PHE 0.010 0.001 PHE B 474 TYR 0.009 0.001 TYR A 140 ARG 0.001 0.000 ARG B 159 *********************** 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 131 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8504 (t0) cc_final: 0.8058 (t0) REVERT: A 234 TRP cc_start: 0.6976 (t-100) cc_final: 0.6520 (t60) REVERT: B 176 ASP cc_start: 0.8484 (t0) cc_final: 0.8052 (t0) REVERT: B 234 TRP cc_start: 0.6980 (t-100) cc_final: 0.6523 (t60) REVERT: B 331 ASP cc_start: 0.8032 (m-30) cc_final: 0.7551 (m-30) outliers start: 16 outliers final: 16 residues processed: 129 average time/residue: 0.2869 time to fit residues: 57.0997 Evaluate side-chains 130 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 94 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: 1.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7796 Z= 0.195 Angle : 0.529 4.591 10602 Z= 0.285 Chirality : 0.040 0.179 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.353 57.278 1062 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.47 % Favored : 93.33 % Rotamer: Outliers : 2.15 % Allowed : 19.24 % 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: 0.64 (0.28), residues: 974 helix: 0.98 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.46 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 344 HIS 0.007 0.001 HIS B 112 PHE 0.010 0.001 PHE A 474 TYR 0.008 0.001 TYR A 140 ARG 0.001 0.000 ARG A 184 *********************** 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 133 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8467 (t0) cc_final: 0.8042 (t0) REVERT: A 234 TRP cc_start: 0.6953 (t-100) cc_final: 0.6483 (t60) REVERT: B 176 ASP cc_start: 0.8456 (t0) cc_final: 0.8153 (t0) REVERT: B 234 TRP cc_start: 0.6960 (t-100) cc_final: 0.6493 (t60) REVERT: B 331 ASP cc_start: 0.8023 (m-30) cc_final: 0.7536 (m-30) outliers start: 17 outliers final: 15 residues processed: 129 average time/residue: 0.2918 time to fit residues: 57.9410 Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 94 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 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: 0.8501 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7796 Z= 0.229 Angle : 0.536 4.517 10602 Z= 0.290 Chirality : 0.040 0.183 1242 Planarity : 0.005 0.043 1254 Dihedral : 5.262 50.375 1062 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.60 % Favored : 92.20 % Rotamer: Outliers : 1.77 % Allowed : 19.62 % 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: 0.56 (0.28), residues: 974 helix: 0.96 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.74 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.007 0.001 HIS A 112 PHE 0.010 0.001 PHE B 474 TYR 0.008 0.001 TYR A 140 ARG 0.001 0.000 ARG B 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 132 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8488 (t0) cc_final: 0.8043 (t0) REVERT: A 234 TRP cc_start: 0.6955 (t-100) cc_final: 0.6475 (t60) REVERT: B 148 MET cc_start: 0.7461 (tpt) cc_final: 0.7255 (ttt) REVERT: B 176 ASP cc_start: 0.8477 (t0) cc_final: 0.8061 (t0) REVERT: B 234 TRP cc_start: 0.6951 (t-100) cc_final: 0.6478 (t60) REVERT: B 331 ASP cc_start: 0.8037 (m-30) cc_final: 0.7546 (m-30) outliers start: 14 outliers final: 14 residues processed: 130 average time/residue: 0.2904 time to fit residues: 58.5508 Evaluate side-chains 131 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 375 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 94 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 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 213 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118774 restraints weight = 32849.912| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.04 r_work: 0.3345 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7796 Z= 0.163 Angle : 0.512 4.565 10602 Z= 0.274 Chirality : 0.039 0.175 1242 Planarity : 0.005 0.042 1254 Dihedral : 5.032 41.378 1062 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.84 % Rotamer: Outliers : 1.77 % Allowed : 20.00 % Favored : 78.23 % 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: 0.69 (0.28), residues: 974 helix: 1.05 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.72 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 344 HIS 0.008 0.002 HIS B 112 PHE 0.010 0.001 PHE A 474 TYR 0.006 0.001 TYR A 140 ARG 0.001 0.000 ARG A 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3819.60 seconds wall clock time: 69 minutes 10.83 seconds (4150.83 seconds total)