Starting phenix.real_space_refine on Wed Feb 14 10:04:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn5_14801/02_2024/7zn5_14801_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn5_14801/02_2024/7zn5_14801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn5_14801/02_2024/7zn5_14801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn5_14801/02_2024/7zn5_14801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn5_14801/02_2024/7zn5_14801_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zn5_14801/02_2024/7zn5_14801_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 18 5.16 5 C 5500 2.51 5 N 1562 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9046 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3533 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3525 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 430, 3525 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3601 Chain: "B" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3566 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 972 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Time building chain proxies: 6.51, per 1000 atoms: 0.72 Number of scatterers: 9046 At special positions: 0 Unit cell: (146.685, 98.679, 89.789, 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 18 16.00 P 97 15.00 O 1869 8.00 N 1562 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.7 seconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 10 sheets defined 40.1% alpha, 9.2% beta 13 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 4.267A pdb=" N TYR A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 48 No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.773A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 205 through 211 removed outlier: 4.153A pdb=" N HIS A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.927A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 382 removed outlier: 4.583A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'B' and resid 16 through 30 removed outlier: 4.349A pdb=" N TYR B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.814A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 189 removed outlier: 4.002A pdb=" N LEU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 removed outlier: 4.399A pdb=" N HIS B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.693A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 380 Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'B' and resid 451 through 461 Processing sheet with id= A, first strand: chain 'A' and resid 69 through 72 removed outlier: 4.121A pdb=" N GLY A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.822A pdb=" N PHE A 109 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 172 through 175 Processing sheet with id= D, first strand: chain 'A' and resid 215 through 219 removed outlier: 7.113A pdb=" N VAL A 238 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N GLU A 198 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N TYR A 240 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N TYR A 272 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR A 241 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 274 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.691A pdb=" N LEU A 388 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= G, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.597A pdb=" N GLY B 175 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 194 through 196 removed outlier: 6.411A pdb=" N ASP B 215 " --> pdb=" O TYR B 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 238 through 241 removed outlier: 7.456A pdb=" N TYR B 272 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR B 241 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 274 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 387 through 389 removed outlier: 3.874A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2318 1.34 - 1.45: 2259 1.45 - 1.57: 4657 1.57 - 1.69: 190 1.69 - 1.81: 32 Bond restraints: 9456 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.730 1.544 0.186 2.00e-02 2.50e+03 8.69e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.730 1.545 0.185 2.00e-02 2.50e+03 8.54e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.313 1.432 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.313 1.432 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" OP2 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.586 1.477 0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 9451 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 840 107.22 - 113.91: 5215 113.91 - 120.60: 3885 120.60 - 127.29: 3059 127.29 - 133.98: 216 Bond angle restraints: 13215 Sorted by residual: angle pdb=" CA ARG B 138 " pdb=" CB ARG B 138 " pdb=" CG ARG B 138 " ideal model delta sigma weight residual 114.10 121.66 -7.56 2.00e+00 2.50e-01 1.43e+01 angle pdb=" CE LLP A 309 " pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 120.00 108.86 11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " pdb=" C4 LLP A 309 " ideal model delta sigma weight residual 120.00 108.96 11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.00 108.98 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CE LLP B 309 " pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 120.00 109.88 10.12 3.00e+00 1.11e-01 1.14e+01 ... (remaining 13210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 5028 32.07 - 64.13: 381 64.13 - 96.20: 19 96.20 - 128.27: 0 128.27 - 160.34: 2 Dihedral angle restraints: 5430 sinusoidal: 2873 harmonic: 2557 Sorted by residual: dihedral pdb=" CG LLP B 309 " pdb=" CD LLP B 309 " pdb=" CE LLP B 309 " pdb=" NZ LLP B 309 " ideal model delta sinusoidal sigma weight residual 119.81 -40.53 160.34 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA ARG A 74 " pdb=" C ARG A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C4' DA D 33 " pdb=" C3' DA D 33 " pdb=" O3' DA D 33 " pdb=" P DA D 34 " ideal model delta sinusoidal sigma weight residual 220.00 78.94 141.06 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 5427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1046 0.032 - 0.064: 255 0.064 - 0.096: 94 0.096 - 0.128: 49 0.128 - 0.159: 6 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CA ARG B 138 " pdb=" N ARG B 138 " pdb=" C ARG B 138 " pdb=" CB ARG B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA GLU B 154 " pdb=" N GLU B 154 " pdb=" C GLU B 154 " pdb=" CB GLU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1447 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " -0.156 2.00e-02 2.50e+03 2.55e-01 6.53e+02 pdb=" NZ LLP A 309 " 0.341 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " -0.320 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " 0.089 2.00e-02 2.50e+03 8.51e-02 7.24e+01 pdb=" NZ LLP B 309 " -0.091 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " 0.081 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 168 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 169 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.027 5.00e-02 4.00e+02 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 807 2.74 - 3.28: 8603 3.28 - 3.82: 15168 3.82 - 4.36: 17077 4.36 - 4.90: 27851 Nonbonded interactions: 69506 Sorted by model distance: nonbonded pdb=" OG SER A 254 " pdb=" OD1 ASN A 256 " model vdw 2.205 2.440 nonbonded pdb=" OG SER A 162 " pdb=" OE2 GLU A 281 " model vdw 2.249 2.440 nonbonded pdb=" OE1 GLN B 184 " pdb=" OH TYR B 330 " model vdw 2.262 2.440 nonbonded pdb=" O HIS B 145 " pdb=" OG SER B 339 " model vdw 2.265 2.440 nonbonded pdb=" O THR B 131 " pdb=" ND2 ASN B 136 " model vdw 2.302 2.520 ... (remaining 69501 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' and (resid 15 through 442 or resid 444 through 464)) selection = (chain 'B' and (resid 15 through 442 or resid 444 through 464)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.280 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.006 0.186 9456 Z= 0.373 Angle : 0.583 11.142 13215 Z= 0.311 Chirality : 0.037 0.159 1450 Planarity : 0.009 0.255 1348 Dihedral : 19.245 160.336 3794 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.13 % Allowed : 0.52 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.18 (0.30), residues: 852 helix: 1.18 (0.28), residues: 374 sheet: 0.15 (0.52), residues: 106 loop : -0.97 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 113 PHE 0.011 0.001 PHE A 128 TYR 0.019 0.001 TYR A 82 ARG 0.003 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8787 (pt) cc_final: 0.8579 (mt) REVERT: A 270 ASN cc_start: 0.7690 (t0) cc_final: 0.7390 (t0) REVERT: B 270 ASN cc_start: 0.7313 (t0) cc_final: 0.6887 (t0) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.2466 time to fit residues: 33.4306 Evaluate side-chains 66 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 73 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 183 GLN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 62 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9456 Z= 0.276 Angle : 0.638 7.110 13215 Z= 0.356 Chirality : 0.043 0.158 1450 Planarity : 0.005 0.048 1348 Dihedral : 20.881 139.238 2060 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.22 % Allowed : 7.83 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.13 (0.29), residues: 852 helix: 0.87 (0.27), residues: 377 sheet: -0.38 (0.49), residues: 113 loop : -0.96 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 264 HIS 0.006 0.001 HIS B 23 PHE 0.018 0.002 PHE A 352 TYR 0.022 0.002 TYR B 21 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7650 (pt0) REVERT: A 33 ILE cc_start: 0.8753 (pt) cc_final: 0.8518 (tt) REVERT: A 270 ASN cc_start: 0.7833 (t0) cc_final: 0.7380 (t0) REVERT: B 62 GLN cc_start: 0.6187 (OUTLIER) cc_final: 0.4936 (tp40) REVERT: B 268 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.7194 (t-90) REVERT: B 270 ASN cc_start: 0.7417 (t0) cc_final: 0.6931 (t0) REVERT: B 346 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6654 (tt0) outliers start: 17 outliers final: 12 residues processed: 79 average time/residue: 0.2234 time to fit residues: 24.8841 Evaluate side-chains 74 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 0.0000 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9456 Z= 0.212 Angle : 0.584 5.352 13215 Z= 0.332 Chirality : 0.041 0.149 1450 Planarity : 0.005 0.049 1348 Dihedral : 21.049 142.564 2060 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.39 % Allowed : 9.14 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.09 (0.29), residues: 852 helix: 0.89 (0.27), residues: 376 sheet: -0.35 (0.49), residues: 113 loop : -0.91 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 264 HIS 0.006 0.001 HIS B 23 PHE 0.011 0.002 PHE A 352 TYR 0.019 0.001 TYR B 21 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 61 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7786 (t0) cc_final: 0.7292 (t0) REVERT: B 268 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.7169 (t-90) REVERT: B 270 ASN cc_start: 0.7501 (t0) cc_final: 0.6997 (t0) outliers start: 26 outliers final: 20 residues processed: 82 average time/residue: 0.2193 time to fit residues: 25.2118 Evaluate side-chains 79 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9456 Z= 0.200 Angle : 0.572 7.240 13215 Z= 0.326 Chirality : 0.040 0.149 1450 Planarity : 0.005 0.049 1348 Dihedral : 21.267 143.837 2060 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.26 % Allowed : 11.62 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.02 (0.29), residues: 852 helix: 0.99 (0.27), residues: 376 sheet: -0.35 (0.50), residues: 113 loop : -0.91 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 264 HIS 0.007 0.001 HIS B 23 PHE 0.010 0.002 PHE A 128 TYR 0.016 0.001 TYR B 17 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7372 (tp) REVERT: A 270 ASN cc_start: 0.7775 (t0) cc_final: 0.7237 (t0) REVERT: B 70 GLU cc_start: 0.8439 (tp30) cc_final: 0.8012 (pm20) REVERT: B 268 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.7142 (t-90) REVERT: B 270 ASN cc_start: 0.7546 (t0) cc_final: 0.7051 (t0) outliers start: 25 outliers final: 20 residues processed: 75 average time/residue: 0.2291 time to fit residues: 23.9716 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 406 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9456 Z= 0.195 Angle : 0.561 5.766 13215 Z= 0.320 Chirality : 0.040 0.150 1450 Planarity : 0.005 0.049 1348 Dihedral : 21.397 144.658 2060 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.39 % Allowed : 13.45 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.01 (0.29), residues: 852 helix: 1.00 (0.27), residues: 376 sheet: -0.32 (0.50), residues: 113 loop : -0.93 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.007 0.001 HIS B 23 PHE 0.011 0.002 PHE A 352 TYR 0.015 0.001 TYR B 17 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 61 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7730 (t0) cc_final: 0.7216 (t0) REVERT: B 70 GLU cc_start: 0.8463 (tp30) cc_final: 0.8026 (pm20) REVERT: B 268 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.7151 (t-90) REVERT: B 270 ASN cc_start: 0.7575 (t0) cc_final: 0.7084 (t0) outliers start: 26 outliers final: 24 residues processed: 80 average time/residue: 0.2231 time to fit residues: 24.7411 Evaluate side-chains 83 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 58 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 406 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9456 Z= 0.158 Angle : 0.542 6.238 13215 Z= 0.310 Chirality : 0.039 0.147 1450 Planarity : 0.005 0.049 1348 Dihedral : 21.464 145.333 2060 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.87 % Allowed : 14.62 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.16 (0.29), residues: 852 helix: 1.13 (0.28), residues: 377 sheet: -0.18 (0.51), residues: 113 loop : -0.85 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.008 0.001 HIS B 23 PHE 0.008 0.001 PHE A 128 TYR 0.015 0.001 TYR B 17 ARG 0.002 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7422 (pt0) REVERT: A 270 ASN cc_start: 0.7721 (t0) cc_final: 0.7228 (t0) REVERT: B 17 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.6572 (t80) REVERT: B 70 GLU cc_start: 0.8418 (tp30) cc_final: 0.8019 (pm20) REVERT: B 268 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.7084 (t-90) REVERT: B 270 ASN cc_start: 0.7554 (t0) cc_final: 0.7063 (t0) outliers start: 22 outliers final: 18 residues processed: 74 average time/residue: 0.2385 time to fit residues: 24.6629 Evaluate side-chains 79 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 406 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9456 Z= 0.252 Angle : 0.604 5.954 13215 Z= 0.341 Chirality : 0.041 0.162 1450 Planarity : 0.005 0.065 1348 Dihedral : 21.772 145.784 2060 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.70 % Allowed : 13.32 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.11 (0.29), residues: 852 helix: 0.92 (0.27), residues: 374 sheet: -0.18 (0.54), residues: 106 loop : -1.04 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 124 HIS 0.008 0.001 HIS B 23 PHE 0.015 0.002 PHE B 352 TYR 0.014 0.002 TYR B 17 ARG 0.013 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 62 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7713 (t0) cc_final: 0.7223 (t0) REVERT: B 17 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6520 (t80) REVERT: B 70 GLU cc_start: 0.8426 (tp30) cc_final: 0.7934 (pm20) REVERT: B 141 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7253 (pp) REVERT: B 270 ASN cc_start: 0.7633 (t0) cc_final: 0.7136 (t0) outliers start: 36 outliers final: 24 residues processed: 90 average time/residue: 0.2214 time to fit residues: 27.8980 Evaluate side-chains 86 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 406 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9456 Z= 0.148 Angle : 0.539 6.547 13215 Z= 0.307 Chirality : 0.039 0.144 1450 Planarity : 0.005 0.049 1348 Dihedral : 21.795 146.187 2060 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.00 % Allowed : 15.40 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.22 (0.30), residues: 852 helix: 1.22 (0.28), residues: 375 sheet: -0.08 (0.51), residues: 115 loop : -0.88 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 124 HIS 0.009 0.001 HIS B 23 PHE 0.008 0.001 PHE A 128 TYR 0.015 0.001 TYR B 17 ARG 0.002 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7646 (t0) cc_final: 0.7205 (t0) REVERT: B 17 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6396 (t80) REVERT: B 270 ASN cc_start: 0.7596 (t0) cc_final: 0.7110 (t0) REVERT: B 414 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8210 (mmtt) outliers start: 23 outliers final: 18 residues processed: 81 average time/residue: 0.2086 time to fit residues: 24.1825 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 406 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 19 GLN B 23 HIS ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9456 Z= 0.302 Angle : 0.643 6.383 13215 Z= 0.360 Chirality : 0.044 0.167 1450 Planarity : 0.005 0.047 1348 Dihedral : 22.077 145.771 2060 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.52 % Allowed : 14.88 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.32 (0.29), residues: 852 helix: 0.75 (0.27), residues: 375 sheet: -0.32 (0.54), residues: 106 loop : -1.14 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 124 HIS 0.007 0.002 HIS A 110 PHE 0.018 0.003 PHE A 352 TYR 0.016 0.002 TYR B 319 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 59 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7914 (pt0) REVERT: A 270 ASN cc_start: 0.7667 (t0) cc_final: 0.7231 (t0) REVERT: B 17 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6883 (t80) REVERT: B 270 ASN cc_start: 0.7676 (t0) cc_final: 0.7163 (t0) outliers start: 27 outliers final: 22 residues processed: 79 average time/residue: 0.2130 time to fit residues: 23.7728 Evaluate side-chains 81 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 406 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9456 Z= 0.191 Angle : 0.575 6.804 13215 Z= 0.324 Chirality : 0.040 0.152 1450 Planarity : 0.005 0.048 1348 Dihedral : 22.072 145.759 2060 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.26 % Allowed : 15.54 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.07 (0.29), residues: 852 helix: 1.01 (0.27), residues: 375 sheet: -0.20 (0.54), residues: 106 loop : -1.07 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 124 HIS 0.006 0.001 HIS B 110 PHE 0.016 0.001 PHE B 119 TYR 0.015 0.001 TYR B 17 ARG 0.003 0.000 ARG B 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.903 Fit side-chains REVERT: A 270 ASN cc_start: 0.7625 (t0) cc_final: 0.7242 (t0) REVERT: A 353 MET cc_start: 0.7171 (ptt) cc_final: 0.6860 (ttp) REVERT: B 17 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6831 (t80) REVERT: B 270 ASN cc_start: 0.7613 (t0) cc_final: 0.7110 (t0) REVERT: B 414 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8254 (mmtt) outliers start: 25 outliers final: 21 residues processed: 82 average time/residue: 0.2147 time to fit residues: 24.7713 Evaluate side-chains 82 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 406 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.139730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109050 restraints weight = 17283.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111888 restraints weight = 9288.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.113745 restraints weight = 6004.142| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 9456 Z= 0.256 Angle : 0.904 59.198 13215 Z= 0.544 Chirality : 0.045 0.807 1450 Planarity : 0.005 0.048 1348 Dihedral : 22.080 145.763 2060 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.89 % Rotamer: Outliers : 3.26 % Allowed : 16.19 % Favored : 80.55 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 5.26 % 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 (0.29), residues: 852 helix: 1.06 (0.27), residues: 375 sheet: -0.20 (0.54), residues: 106 loop : -1.07 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.005 0.001 HIS B 110 PHE 0.014 0.001 PHE B 119 TYR 0.015 0.001 TYR B 17 ARG 0.003 0.000 ARG B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1837.86 seconds wall clock time: 34 minutes 12.76 seconds (2052.76 seconds total)