Starting phenix.real_space_refine on Fri Aug 2 18:23:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yjy_39353/08_2024/8yjy_39353.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yjy_39353/08_2024/8yjy_39353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yjy_39353/08_2024/8yjy_39353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yjy_39353/08_2024/8yjy_39353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yjy_39353/08_2024/8yjy_39353.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yjy_39353/08_2024/8yjy_39353.cif" } resolution = 3.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2701 2.51 5 N 760 2.21 5 O 783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4254 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2969 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 18, 'TRANS': 354} Chain breaks: 2 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 143} Time building chain proxies: 3.34, per 1000 atoms: 0.79 Number of scatterers: 4254 At special positions: 0 Unit cell: (64.32, 69.68, 119.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 783 8.00 N 760 7.00 C 2701 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: 1.60 Conformation dependent library (CDL) restraints added in 710.5 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 50.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.527A pdb=" N LYS A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 52 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 91 through 95 removed outlier: 3.862A pdb=" N THR A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.827A pdb=" N HIS A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 removed outlier: 4.104A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.720A pdb=" N TYR A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 3.711A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 232 " --> pdb=" O TRP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 242 through 261 Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.618A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 removed outlier: 3.772A pdb=" N ILE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 311 through 337 removed outlier: 3.650A pdb=" N TYR A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 352 through 374 removed outlier: 3.845A pdb=" N VAL A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 removed outlier: 3.796A pdb=" N ARG B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B 22 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS B 23 " --> pdb=" O TYR B 19 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 121 through 141 removed outlier: 4.125A pdb=" N THR B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Proline residue: B 128 - end of helix removed outlier: 3.542A pdb=" N GLU B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 66 removed outlier: 3.693A pdb=" N TYR A 64 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 88 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 86 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 137 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA3, first strand: chain 'A' and resid 283 through 285 removed outlier: 3.612A pdb=" N VAL A 283 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 removed outlier: 4.135A pdb=" N ARG B 30 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 43 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 34 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 61 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 44 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER B 62 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N CYS B 69 " --> pdb=" O LEU B 100 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 549 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: 1.10 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1420 1.34 - 1.46: 916 1.46 - 1.58: 2014 1.58 - 1.69: 1 1.69 - 1.81: 14 Bond restraints: 4365 Sorted by residual: bond pdb=" CB PRO B 12 " pdb=" CG PRO B 12 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.02e+00 bond pdb=" N PRO B 12 " pdb=" CA PRO B 12 " ideal model delta sigma weight residual 1.469 1.453 0.015 1.28e-02 6.10e+03 1.42e+00 bond pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.32e+00 bond pdb=" C VAL B 158 " pdb=" O VAL B 158 " ideal model delta sigma weight residual 1.241 1.232 0.010 1.06e-02 8.90e+03 8.20e-01 bond pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta sigma weight residual 1.469 1.479 -0.010 1.28e-02 6.10e+03 6.72e-01 ... (remaining 4360 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.57: 89 104.57 - 111.94: 2168 111.94 - 119.32: 1429 119.32 - 126.69: 2151 126.69 - 134.07: 102 Bond angle restraints: 5939 Sorted by residual: angle pdb=" CA PRO B 12 " pdb=" N PRO B 12 " pdb=" CD PRO B 12 " ideal model delta sigma weight residual 112.00 97.35 14.65 1.40e+00 5.10e-01 1.10e+02 angle pdb=" C GLY B 81 " pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" N PRO B 12 " pdb=" CD PRO B 12 " pdb=" CG PRO B 12 " ideal model delta sigma weight residual 103.20 97.19 6.01 1.50e+00 4.44e-01 1.60e+01 angle pdb=" CA LEU A 58 " pdb=" CB LEU A 58 " pdb=" CG LEU A 58 " ideal model delta sigma weight residual 116.30 128.71 -12.41 3.50e+00 8.16e-02 1.26e+01 angle pdb=" N THR B 82 " pdb=" CA THR B 82 " pdb=" CB THR B 82 " ideal model delta sigma weight residual 110.49 115.19 -4.70 1.69e+00 3.50e-01 7.74e+00 ... (remaining 5934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 2227 17.62 - 35.25: 270 35.25 - 52.87: 81 52.87 - 70.49: 15 70.49 - 88.11: 7 Dihedral angle restraints: 2600 sinusoidal: 1056 harmonic: 1544 Sorted by residual: dihedral pdb=" CA ALA A 132 " pdb=" C ALA A 132 " pdb=" N GLY A 133 " pdb=" CA GLY A 133 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA HIS A 290 " pdb=" C HIS A 290 " pdb=" N VAL A 291 " pdb=" CA VAL A 291 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA VAL A 291 " pdb=" C VAL A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 2597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 443 0.032 - 0.063: 126 0.063 - 0.095: 45 0.095 - 0.126: 26 0.126 - 0.158: 7 Chirality restraints: 647 Sorted by residual: chirality pdb=" CA THR A 354 " pdb=" N THR A 354 " pdb=" C THR A 354 " pdb=" CB THR A 354 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA THR B 82 " pdb=" N THR B 82 " pdb=" C THR B 82 " pdb=" CB THR B 82 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 644 not shown) Planarity restraints: 770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 11 " -0.104 5.00e-02 4.00e+02 1.46e-01 3.40e+01 pdb=" N PRO B 12 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 12 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 12 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 153 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 154 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 154 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 154 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 313 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 314 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 314 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 314 " -0.025 5.00e-02 4.00e+02 ... (remaining 767 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 177 2.72 - 3.26: 4235 3.26 - 3.81: 6728 3.81 - 4.35: 7846 4.35 - 4.90: 13518 Nonbonded interactions: 32504 Sorted by model distance: nonbonded pdb=" O GLN B 139 " pdb=" OG1 THR B 143 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR B 14 " pdb=" OE1 GLN B 17 " model vdw 2.187 3.040 nonbonded pdb=" N ILE A 289 " pdb=" OD1 ASN A 306 " model vdw 2.260 3.120 nonbonded pdb=" O ARG A 362 " pdb=" ND1 HIS A 366 " model vdw 2.262 3.120 nonbonded pdb=" O SER A 243 " pdb=" OG1 THR A 247 " model vdw 2.304 3.040 ... (remaining 32499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 4365 Z= 0.277 Angle : 0.744 14.651 5939 Z= 0.413 Chirality : 0.041 0.158 647 Planarity : 0.008 0.146 770 Dihedral : 17.276 88.115 1602 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.22 % Allowed : 23.74 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.36), residues: 522 helix: 2.48 (0.37), residues: 200 sheet: 0.88 (0.56), residues: 73 loop : -0.23 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 164 HIS 0.004 0.001 HIS B 87 PHE 0.015 0.002 PHE B 137 TYR 0.020 0.002 TYR A 43 ARG 0.007 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.478 Fit side-chains REVERT: A 365 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6244 (mp0) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2233 time to fit residues: 13.9012 Evaluate side-chains 49 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4365 Z= 0.240 Angle : 0.639 9.485 5939 Z= 0.327 Chirality : 0.043 0.156 647 Planarity : 0.006 0.065 770 Dihedral : 4.688 21.180 580 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.42 % Allowed : 23.30 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.74 (0.37), residues: 522 helix: 2.51 (0.35), residues: 226 sheet: 1.36 (0.70), residues: 51 loop : -0.18 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 323 HIS 0.004 0.001 HIS A 324 PHE 0.013 0.002 PHE B 137 TYR 0.022 0.002 TYR A 43 ARG 0.005 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.468 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 0.1669 time to fit residues: 12.6166 Evaluate side-chains 54 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4365 Z= 0.239 Angle : 0.639 9.682 5939 Z= 0.325 Chirality : 0.044 0.151 647 Planarity : 0.005 0.047 770 Dihedral : 4.709 20.486 580 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.18 % Allowed : 21.76 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.62 (0.37), residues: 522 helix: 2.38 (0.35), residues: 226 sheet: 1.06 (0.63), residues: 66 loop : -0.24 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 323 HIS 0.004 0.001 HIS A 324 PHE 0.012 0.002 PHE A 281 TYR 0.022 0.002 TYR A 43 ARG 0.004 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.477 Fit side-chains REVERT: A 365 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6183 (mp0) outliers start: 19 outliers final: 7 residues processed: 61 average time/residue: 0.1655 time to fit residues: 12.8972 Evaluate side-chains 55 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4365 Z= 0.221 Angle : 0.618 7.974 5939 Z= 0.315 Chirality : 0.043 0.149 647 Planarity : 0.005 0.044 770 Dihedral : 4.628 21.444 580 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.40 % Allowed : 23.52 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.57 (0.38), residues: 522 helix: 2.40 (0.35), residues: 229 sheet: 0.91 (0.63), residues: 66 loop : -0.32 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 136 PHE 0.011 0.002 PHE A 281 TYR 0.020 0.002 TYR A 43 ARG 0.003 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.644 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 58 average time/residue: 0.1520 time to fit residues: 11.4594 Evaluate side-chains 53 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4365 Z= 0.207 Angle : 0.592 7.811 5939 Z= 0.299 Chirality : 0.043 0.149 647 Planarity : 0.005 0.043 770 Dihedral : 4.510 21.228 580 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.84 % Allowed : 23.96 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.69 (0.38), residues: 522 helix: 2.55 (0.35), residues: 229 sheet: 0.87 (0.65), residues: 61 loop : -0.27 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.003 0.001 HIS A 136 PHE 0.010 0.001 PHE A 281 TYR 0.020 0.002 TYR A 43 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 0.480 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 61 average time/residue: 0.1625 time to fit residues: 12.9017 Evaluate side-chains 58 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.0070 chunk 36 optimal weight: 0.3980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4365 Z= 0.156 Angle : 0.556 7.119 5939 Z= 0.282 Chirality : 0.042 0.163 647 Planarity : 0.005 0.043 770 Dihedral : 4.312 21.055 580 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.30 % Allowed : 25.05 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.38), residues: 522 helix: 2.77 (0.36), residues: 223 sheet: 1.00 (0.65), residues: 61 loop : -0.30 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.002 0.000 HIS A 136 PHE 0.008 0.001 PHE A 281 TYR 0.020 0.001 TYR A 43 ARG 0.002 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.457 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 56 average time/residue: 0.1728 time to fit residues: 12.2778 Evaluate side-chains 54 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4365 Z= 0.197 Angle : 0.621 12.701 5939 Z= 0.301 Chirality : 0.043 0.159 647 Planarity : 0.005 0.043 770 Dihedral : 4.315 20.959 580 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.08 % Allowed : 25.49 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.73 (0.38), residues: 522 helix: 2.61 (0.36), residues: 229 sheet: 0.80 (0.65), residues: 61 loop : -0.26 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 116 HIS 0.003 0.001 HIS A 136 PHE 0.009 0.001 PHE A 281 TYR 0.019 0.002 TYR A 43 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.481 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 55 average time/residue: 0.1859 time to fit residues: 13.0786 Evaluate side-chains 58 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4365 Z= 0.210 Angle : 0.615 11.173 5939 Z= 0.301 Chirality : 0.043 0.164 647 Planarity : 0.005 0.043 770 Dihedral : 4.369 21.073 580 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.86 % Allowed : 24.84 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.58 (0.38), residues: 522 helix: 2.53 (0.36), residues: 228 sheet: 0.62 (0.65), residues: 61 loop : -0.34 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.003 0.001 HIS A 136 PHE 0.010 0.001 PHE A 281 TYR 0.018 0.002 TYR A 43 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.460 Fit side-chains REVERT: A 296 MET cc_start: 0.6761 (mmt) cc_final: 0.6518 (mmt) outliers start: 13 outliers final: 12 residues processed: 55 average time/residue: 0.1800 time to fit residues: 12.4611 Evaluate side-chains 54 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 0.0040 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4365 Z= 0.181 Angle : 0.603 11.195 5939 Z= 0.295 Chirality : 0.043 0.171 647 Planarity : 0.005 0.043 770 Dihedral : 4.233 20.872 580 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.98 % Allowed : 25.27 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.67 (0.38), residues: 522 helix: 2.68 (0.36), residues: 228 sheet: 0.54 (0.64), residues: 61 loop : -0.33 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 116 HIS 0.002 0.001 HIS A 136 PHE 0.008 0.001 PHE A 281 TYR 0.019 0.001 TYR A 43 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.481 Fit side-chains REVERT: A 296 MET cc_start: 0.6652 (mmt) cc_final: 0.6363 (mmt) outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.1959 time to fit residues: 11.8773 Evaluate side-chains 50 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4365 Z= 0.208 Angle : 0.619 10.698 5939 Z= 0.302 Chirality : 0.043 0.164 647 Planarity : 0.005 0.043 770 Dihedral : 4.311 21.253 580 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.64 % Allowed : 24.40 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.38), residues: 522 helix: 2.61 (0.36), residues: 228 sheet: 0.39 (0.65), residues: 61 loop : -0.39 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 116 HIS 0.004 0.001 HIS A 366 PHE 0.009 0.001 PHE A 281 TYR 0.019 0.001 TYR A 43 ARG 0.002 0.000 ARG A 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.469 Fit side-chains REVERT: A 59 GLN cc_start: 0.8039 (tt0) cc_final: 0.7574 (mt0) REVERT: A 296 MET cc_start: 0.6776 (mmt) cc_final: 0.6429 (mmt) outliers start: 12 outliers final: 11 residues processed: 55 average time/residue: 0.1780 time to fit residues: 12.4289 Evaluate side-chains 56 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.0070 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.227465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.189744 restraints weight = 5186.104| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.56 r_work: 0.4142 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4365 Z= 0.177 Angle : 0.605 10.718 5939 Z= 0.292 Chirality : 0.042 0.175 647 Planarity : 0.005 0.043 770 Dihedral : 4.153 21.000 580 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.20 % Allowed : 24.84 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.65 (0.39), residues: 522 helix: 2.70 (0.36), residues: 228 sheet: 0.30 (0.64), residues: 61 loop : -0.32 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 116 HIS 0.004 0.001 HIS A 366 PHE 0.008 0.001 PHE A 281 TYR 0.019 0.001 TYR A 43 ARG 0.002 0.000 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1438.19 seconds wall clock time: 25 minutes 57.05 seconds (1557.05 seconds total)