Starting phenix.real_space_refine on Tue Mar 11 23:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l0p_23099/03_2025/7l0p_23099.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l0p_23099/03_2025/7l0p_23099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l0p_23099/03_2025/7l0p_23099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l0p_23099/03_2025/7l0p_23099.map" model { file = "/net/cci-nas-00/data/ceres_data/7l0p_23099/03_2025/7l0p_23099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l0p_23099/03_2025/7l0p_23099.cif" } resolution = 4.1 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= 0.003 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 52 5.16 5 C 4442 2.51 5 N 1173 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6953 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2409 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2385 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 305} Chain: "G" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 310 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Time building chain proxies: 4.45, per 1000 atoms: 0.64 Number of scatterers: 6953 At special positions: 0 Unit cell: (75.075, 109.725, 124.575, 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 52 16.00 O 1286 8.00 N 1173 7.00 C 4442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 225 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.56 Conformation dependent library (CDL) restraints added in 959.1 milliseconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 11 sheets defined 42.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 60 through 90 Processing helix chain 'C' and resid 102 through 128 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 138 through 172 Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 182 through 206 Proline residue: C 203 - end of helix Processing helix chain 'C' and resid 230 through 269 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 298 through 334 removed outlier: 3.791A pdb=" N VAL C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Proline residue: C 323 - end of helix removed outlier: 3.602A pdb=" N ILE C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 371 Proline residue: C 366 - end of helix Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'A' and resid 4 through 7 Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.572A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 4.064A pdb=" N GLY A 203 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.605A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 removed outlier: 4.755A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 48 Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 222 removed outlier: 6.222A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 222 removed outlier: 6.222A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.631A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.597A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.870A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.760A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 235 removed outlier: 4.573A pdb=" N ALA B 240 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.427A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1050 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: 1.87 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1876 1.33 - 1.46: 1678 1.46 - 1.58: 3463 1.58 - 1.70: 0 1.70 - 1.83: 75 Bond restraints: 7092 Sorted by residual: bond pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.08e-02 8.57e+03 1.16e+01 bond pdb=" N PRO B 236 " pdb=" CA PRO B 236 " ideal model delta sigma weight residual 1.469 1.508 -0.039 1.28e-02 6.10e+03 9.45e+00 bond pdb=" N CYS B 233 " pdb=" CA CYS B 233 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.21e+00 bond pdb=" N TYR C 333 " pdb=" CA TYR C 333 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.31e-02 5.83e+03 5.67e+00 ... (remaining 7087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 9052 1.97 - 3.93: 464 3.93 - 5.90: 57 5.90 - 7.87: 19 7.87 - 9.84: 19 Bond angle restraints: 9611 Sorted by residual: angle pdb=" N PRO C 297 " pdb=" CA PRO C 297 " pdb=" CB PRO C 297 " ideal model delta sigma weight residual 103.25 111.61 -8.36 1.05e+00 9.07e-01 6.34e+01 angle pdb=" C PHE B 235 " pdb=" N PRO B 236 " pdb=" CA PRO B 236 " ideal model delta sigma weight residual 119.84 127.37 -7.53 1.25e+00 6.40e-01 3.63e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.08 129.12 -7.04 1.47e+00 4.63e-01 2.29e+01 angle pdb=" C SER C 335 " pdb=" N ASP C 336 " pdb=" CA ASP C 336 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.26e+01 angle pdb=" CA ASN B 268 " pdb=" CB ASN B 268 " pdb=" CG ASN B 268 " ideal model delta sigma weight residual 112.60 117.29 -4.69 1.00e+00 1.00e+00 2.20e+01 ... (remaining 9606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 3588 16.04 - 32.07: 454 32.07 - 48.10: 122 48.10 - 64.14: 20 64.14 - 80.17: 6 Dihedral angle restraints: 4190 sinusoidal: 1611 harmonic: 2579 Sorted by residual: dihedral pdb=" CA SER B 160 " pdb=" C SER B 160 " pdb=" N SER B 161 " pdb=" CA SER B 161 " ideal model delta harmonic sigma weight residual 180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA LEU B 192 " pdb=" C LEU B 192 " pdb=" N ALA B 193 " pdb=" CA ALA B 193 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE C 248 " pdb=" C PHE C 248 " pdb=" N PRO C 249 " pdb=" CA PRO C 249 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 4187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 813 0.060 - 0.119: 241 0.119 - 0.179: 42 0.179 - 0.239: 13 0.239 - 0.298: 3 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA PRO C 297 " pdb=" N PRO C 297 " pdb=" C PRO C 297 " pdb=" CB PRO C 297 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA HIS C 133 " pdb=" N HIS C 133 " pdb=" C HIS C 133 " pdb=" CB HIS C 133 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASN B 268 " pdb=" N ASN B 268 " pdb=" C ASN B 268 " pdb=" CB ASN B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1109 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 248 " -0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO C 249 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 249 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 249 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 4 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C THR A 4 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 4 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 5 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 340 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C THR A 340 " 0.055 2.00e-02 2.50e+03 pdb=" O THR A 340 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 341 " -0.018 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1280 2.76 - 3.30: 6656 3.30 - 3.83: 11898 3.83 - 4.37: 13500 4.37 - 4.90: 23341 Nonbonded interactions: 56675 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR C 146 " pdb=" OXT LEU D 13 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.297 3.040 nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.298 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.301 3.040 ... (remaining 56670 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 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.220 Find NCS groups from input model: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 0.093 7092 Z= 0.404 Angle : 1.062 9.835 9611 Z= 0.605 Chirality : 0.061 0.298 1112 Planarity : 0.007 0.094 1206 Dihedral : 15.233 80.175 2519 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.78 % Favored : 92.87 % Rotamer: Outliers : 0.53 % Allowed : 13.98 % Favored : 85.49 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.23), residues: 870 helix: -2.20 (0.20), residues: 368 sheet: -2.14 (0.39), residues: 151 loop : -2.90 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 135 HIS 0.005 0.001 HIS A 195 PHE 0.022 0.003 PHE A 189 TYR 0.014 0.002 TYR C 146 ARG 0.008 0.001 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 263 LYS cc_start: 0.6986 (mmmm) cc_final: 0.6619 (ttmt) REVERT: A 248 LYS cc_start: 0.8836 (tppt) cc_final: 0.8597 (tppt) REVERT: A 318 GLU cc_start: 0.8543 (pt0) cc_final: 0.8282 (pt0) REVERT: B 42 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8250 (ttm170) REVERT: B 82 TRP cc_start: 0.8327 (m100) cc_final: 0.7966 (m100) REVERT: B 172 GLU cc_start: 0.6589 (mp0) cc_final: 0.6310 (mp0) REVERT: B 234 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: B 241 PHE cc_start: 0.8760 (p90) cc_final: 0.8351 (p90) REVERT: B 289 TYR cc_start: 0.8566 (m-10) cc_final: 0.8261 (m-10) REVERT: G 55 LYS cc_start: 0.8656 (tttp) cc_final: 0.8015 (mmtt) outliers start: 4 outliers final: 1 residues processed: 225 average time/residue: 0.2226 time to fit residues: 64.0307 Evaluate side-chains 176 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 159 ASN C 348 HIS A 188 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.170910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143901 restraints weight = 8788.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143083 restraints weight = 10286.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144042 restraints weight = 9801.832| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7092 Z= 0.216 Angle : 0.675 8.028 9611 Z= 0.356 Chirality : 0.044 0.187 1112 Planarity : 0.005 0.083 1206 Dihedral : 5.902 59.039 955 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.94 % Favored : 94.83 % Rotamer: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.25), residues: 870 helix: -0.65 (0.24), residues: 376 sheet: -1.88 (0.38), residues: 156 loop : -2.64 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 339 HIS 0.005 0.001 HIS C 133 PHE 0.020 0.002 PHE C 344 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: C 350 PHE cc_start: 0.8000 (t80) cc_final: 0.7769 (t80) REVERT: A 18 MET cc_start: 0.7098 (tpp) cc_final: 0.6822 (ttt) REVERT: A 24 ARG cc_start: 0.6163 (mtt180) cc_final: 0.5686 (mtp-110) REVERT: A 248 LYS cc_start: 0.8527 (tppt) cc_final: 0.8287 (tppt) REVERT: A 304 GLN cc_start: 0.8134 (tt0) cc_final: 0.7735 (tt0) REVERT: B 251 ARG cc_start: 0.7137 (mtt-85) cc_final: 0.6851 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.1888 time to fit residues: 50.6445 Evaluate side-chains 163 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 21 optimal weight: 0.0000 chunk 74 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 0.0370 chunk 37 optimal weight: 0.2980 overall best weight: 0.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 365 ASN A 269 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.150116 restraints weight = 8778.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.150338 restraints weight = 7802.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151086 restraints weight = 6406.019| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7092 Z= 0.166 Angle : 0.614 7.021 9611 Z= 0.320 Chirality : 0.042 0.174 1112 Planarity : 0.005 0.077 1206 Dihedral : 5.372 60.559 955 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.27), residues: 870 helix: 0.04 (0.26), residues: 378 sheet: -1.66 (0.37), residues: 158 loop : -2.27 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 339 HIS 0.005 0.001 HIS C 133 PHE 0.021 0.002 PHE B 234 TYR 0.019 0.001 TYR B 264 ARG 0.006 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8844 (t) cc_final: 0.8603 (t) REVERT: C 327 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7592 (ttp80) REVERT: A 24 ARG cc_start: 0.6117 (mtt180) cc_final: 0.5756 (mtp-110) REVERT: A 204 GLN cc_start: 0.8247 (pp30) cc_final: 0.7989 (pt0) REVERT: A 248 LYS cc_start: 0.8531 (tppt) cc_final: 0.8247 (tppt) REVERT: A 287 TYR cc_start: 0.7403 (m-80) cc_final: 0.7047 (m-10) REVERT: A 304 GLN cc_start: 0.8032 (tt0) cc_final: 0.7819 (tt0) REVERT: A 312 LYS cc_start: 0.8269 (mttt) cc_final: 0.7640 (mmtt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2075 time to fit residues: 55.6725 Evaluate side-chains 166 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 270 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.169002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150499 restraints weight = 8997.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149381 restraints weight = 14837.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147459 restraints weight = 13986.646| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7092 Z= 0.282 Angle : 0.672 6.917 9611 Z= 0.355 Chirality : 0.046 0.174 1112 Planarity : 0.005 0.080 1206 Dihedral : 5.443 54.710 955 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.86 % Favored : 94.02 % Rotamer: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.27), residues: 870 helix: 0.23 (0.26), residues: 379 sheet: -1.91 (0.37), residues: 176 loop : -2.40 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 339 HIS 0.006 0.001 HIS B 62 PHE 0.023 0.002 PHE B 234 TYR 0.011 0.002 TYR B 59 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: C 235 LYS cc_start: 0.5804 (tttt) cc_final: 0.5516 (tptm) REVERT: C 328 ARG cc_start: 0.8244 (mtp180) cc_final: 0.8028 (mtt180) REVERT: A 24 ARG cc_start: 0.6284 (mtt180) cc_final: 0.5891 (mtp-110) REVERT: A 53 MET cc_start: 0.7414 (mmt) cc_final: 0.7125 (mmt) REVERT: A 287 TYR cc_start: 0.7448 (m-80) cc_final: 0.7248 (m-10) REVERT: A 304 GLN cc_start: 0.8210 (tt0) cc_final: 0.7865 (tt0) REVERT: B 251 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.6764 (mtt-85) REVERT: B 263 THR cc_start: 0.8343 (m) cc_final: 0.8045 (m) REVERT: B 264 TYR cc_start: 0.7729 (m-80) cc_final: 0.7350 (m-80) REVERT: B 284 LEU cc_start: 0.8330 (tt) cc_final: 0.8104 (tt) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.2102 time to fit residues: 52.3661 Evaluate side-chains 158 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 365 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.164427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140100 restraints weight = 9062.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139865 restraints weight = 10079.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139849 restraints weight = 10379.294| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7092 Z= 0.302 Angle : 0.689 7.564 9611 Z= 0.363 Chirality : 0.046 0.174 1112 Planarity : 0.005 0.081 1206 Dihedral : 5.620 54.592 955 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.55 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.27), residues: 870 helix: 0.31 (0.26), residues: 377 sheet: -1.91 (0.37), residues: 178 loop : -2.30 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 297 HIS 0.004 0.001 HIS C 133 PHE 0.023 0.002 PHE A 199 TYR 0.019 0.002 TYR B 111 ARG 0.006 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.806 Fit side-chains REVERT: A 24 ARG cc_start: 0.6252 (mtt180) cc_final: 0.5878 (mtp-110) REVERT: A 304 GLN cc_start: 0.8174 (tt0) cc_final: 0.7962 (tt0) REVERT: B 264 TYR cc_start: 0.7742 (m-80) cc_final: 0.7333 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2067 time to fit residues: 50.2274 Evaluate side-chains 153 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 75 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 142 HIS B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150961 restraints weight = 9009.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149140 restraints weight = 15882.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149125 restraints weight = 15044.466| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7092 Z= 0.253 Angle : 0.673 9.566 9611 Z= 0.351 Chirality : 0.045 0.193 1112 Planarity : 0.005 0.079 1206 Dihedral : 5.478 60.558 955 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 0.26 % Allowed : 2.37 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.28), residues: 870 helix: 0.49 (0.26), residues: 378 sheet: -1.83 (0.39), residues: 175 loop : -2.28 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 339 HIS 0.007 0.001 HIS B 142 PHE 0.014 0.002 PHE C 137 TYR 0.018 0.002 TYR B 59 ARG 0.009 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6354 (mtt180) cc_final: 0.5960 (mtp-110) REVERT: A 287 TYR cc_start: 0.7154 (m-80) cc_final: 0.6878 (m-10) REVERT: A 304 GLN cc_start: 0.8088 (tt0) cc_final: 0.7769 (tt0) REVERT: B 264 TYR cc_start: 0.7573 (m-80) cc_final: 0.7248 (m-80) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.2166 time to fit residues: 53.4729 Evaluate side-chains 159 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 84 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3912 r_free = 0.3912 target = 0.168131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150905 restraints weight = 8943.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149525 restraints weight = 15032.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149301 restraints weight = 14734.513| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7092 Z= 0.249 Angle : 0.671 9.910 9611 Z= 0.350 Chirality : 0.045 0.180 1112 Planarity : 0.005 0.078 1206 Dihedral : 5.467 63.127 955 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.28), residues: 870 helix: 0.61 (0.26), residues: 378 sheet: -1.80 (0.39), residues: 177 loop : -2.16 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 297 HIS 0.004 0.001 HIS C 133 PHE 0.021 0.002 PHE A 189 TYR 0.015 0.001 TYR B 59 ARG 0.011 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6364 (mtt180) cc_final: 0.5990 (mtp-110) REVERT: A 53 MET cc_start: 0.7225 (mmt) cc_final: 0.7005 (mmt) REVERT: A 304 GLN cc_start: 0.8106 (tt0) cc_final: 0.7769 (tt0) REVERT: A 321 THR cc_start: 0.8915 (t) cc_final: 0.8331 (t) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2126 time to fit residues: 51.3304 Evaluate side-chains 162 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156535 restraints weight = 8904.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155943 restraints weight = 15943.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156285 restraints weight = 13611.928| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7092 Z= 0.184 Angle : 0.640 10.260 9611 Z= 0.332 Chirality : 0.044 0.222 1112 Planarity : 0.004 0.076 1206 Dihedral : 5.405 74.324 955 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.28), residues: 870 helix: 0.85 (0.26), residues: 372 sheet: -1.71 (0.39), residues: 179 loop : -2.01 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 339 HIS 0.004 0.001 HIS C 133 PHE 0.023 0.002 PHE B 234 TYR 0.019 0.001 TYR A 287 ARG 0.008 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6325 (mtt180) cc_final: 0.5969 (mtp-110) REVERT: A 53 MET cc_start: 0.6953 (mmt) cc_final: 0.6668 (mmt) REVERT: A 198 MET cc_start: 0.8359 (mtp) cc_final: 0.8092 (ttm) REVERT: A 304 GLN cc_start: 0.8024 (tt0) cc_final: 0.7823 (tt0) REVERT: A 312 LYS cc_start: 0.8230 (mttt) cc_final: 0.7906 (mmtt) REVERT: B 110 ASN cc_start: 0.5836 (t0) cc_final: 0.5588 (t0) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.1988 time to fit residues: 50.4457 Evaluate side-chains 161 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154745 restraints weight = 8951.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154133 restraints weight = 14826.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151648 restraints weight = 14276.549| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7092 Z= 0.212 Angle : 0.648 9.931 9611 Z= 0.338 Chirality : 0.045 0.215 1112 Planarity : 0.004 0.076 1206 Dihedral : 5.318 71.259 955 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.29 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.28), residues: 870 helix: 0.91 (0.26), residues: 372 sheet: -1.60 (0.40), residues: 177 loop : -1.93 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 297 HIS 0.006 0.001 HIS C 348 PHE 0.020 0.002 PHE A 189 TYR 0.021 0.002 TYR A 287 ARG 0.008 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8805 (t) cc_final: 0.8550 (t) REVERT: C 310 LEU cc_start: 0.7438 (mp) cc_final: 0.7232 (mp) REVERT: A 24 ARG cc_start: 0.6140 (mtt180) cc_final: 0.5833 (mtp-110) REVERT: A 304 GLN cc_start: 0.8134 (tt0) cc_final: 0.7886 (tt0) REVERT: A 312 LYS cc_start: 0.8316 (mttt) cc_final: 0.7943 (mmtt) REVERT: A 321 THR cc_start: 0.8930 (t) cc_final: 0.8331 (t) REVERT: B 264 TYR cc_start: 0.7577 (m-80) cc_final: 0.7365 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1985 time to fit residues: 48.7507 Evaluate side-chains 161 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 365 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149840 restraints weight = 9158.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147350 restraints weight = 15392.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145178 restraints weight = 16247.345| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7092 Z= 0.261 Angle : 0.674 9.420 9611 Z= 0.353 Chirality : 0.046 0.172 1112 Planarity : 0.005 0.077 1206 Dihedral : 5.471 68.876 955 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.28), residues: 870 helix: 0.85 (0.26), residues: 372 sheet: -1.76 (0.39), residues: 180 loop : -1.96 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 297 HIS 0.006 0.001 HIS C 348 PHE 0.022 0.002 PHE A 189 TYR 0.022 0.002 TYR A 287 ARG 0.007 0.001 ARG C 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 172 CYS cc_start: 0.8006 (t) cc_final: 0.7796 (t) REVERT: C 310 LEU cc_start: 0.7516 (mp) cc_final: 0.7269 (mp) REVERT: C 327 ARG cc_start: 0.7802 (ttp80) cc_final: 0.6983 (ttp80) REVERT: A 24 ARG cc_start: 0.6203 (mtt180) cc_final: 0.5881 (mtp-110) REVERT: A 230 TYR cc_start: 0.7401 (p90) cc_final: 0.7180 (p90) REVERT: A 312 LYS cc_start: 0.8374 (mttt) cc_final: 0.7956 (mmtt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2124 time to fit residues: 51.1144 Evaluate side-chains 151 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3915 r_free = 0.3915 target = 0.168650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148579 restraints weight = 9091.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143491 restraints weight = 11869.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143751 restraints weight = 10314.831| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7092 Z= 0.268 Angle : 0.685 9.245 9611 Z= 0.360 Chirality : 0.047 0.193 1112 Planarity : 0.005 0.077 1206 Dihedral : 5.506 67.430 955 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.44 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.28), residues: 870 helix: 0.77 (0.26), residues: 373 sheet: -1.69 (0.40), residues: 178 loop : -1.89 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 297 HIS 0.007 0.001 HIS C 348 PHE 0.035 0.002 PHE B 235 TYR 0.023 0.002 TYR A 287 ARG 0.007 0.001 ARG C 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2525.14 seconds wall clock time: 44 minutes 41.01 seconds (2681.01 seconds total)