Starting phenix.real_space_refine on Tue Feb 13 16:45:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0p_23099/02_2024/7l0p_23099.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0p_23099/02_2024/7l0p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0p_23099/02_2024/7l0p_23099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0p_23099/02_2024/7l0p_23099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0p_23099/02_2024/7l0p_23099.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0p_23099/02_2024/7l0p_23099.pdb" } 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 Residue "D ARG 8": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 4.31, per 1000 atoms: 0.62 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 - 3.50 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: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.65 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: 2.08 Time building geometry restraints manager: 2.97 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: 96.25 - 103.96: 68 103.96 - 111.66: 3123 111.66 - 119.37: 2780 119.37 - 127.08: 3552 127.08 - 134.79: 88 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 2.440 nonbonded pdb=" OH TYR C 146 " pdb=" OXT LEU D 13 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.297 2.440 nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.298 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.301 2.440 ... (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 ========== 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: 0.890 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: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.480 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 0.789 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: 0.2203 time to fit residues: 63.3809 Evaluate side-chains 176 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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: 0.3980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 241 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7092 Z= 0.219 Angle : 0.660 8.053 9611 Z= 0.347 Chirality : 0.044 0.182 1112 Planarity : 0.005 0.083 1206 Dihedral : 5.865 58.022 955 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.17 % Favored : 94.60 % Rotamer: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % 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: -2.48 (0.26), residues: 870 helix: -0.56 (0.25), residues: 376 sheet: -2.01 (0.37), residues: 166 loop : -2.63 (0.29), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 339 HIS 0.005 0.001 HIS C 133 PHE 0.021 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 202 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 0.836 Fit side-chains REVERT: C 164 SER cc_start: 0.8892 (t) cc_final: 0.8681 (t) REVERT: C 350 PHE cc_start: 0.8235 (t80) cc_final: 0.7872 (t80) REVERT: A 24 ARG cc_start: 0.5753 (mtt180) cc_final: 0.5197 (mtp-110) REVERT: A 191 PHE cc_start: 0.6899 (t80) cc_final: 0.6681 (t80) REVERT: A 248 LYS cc_start: 0.8772 (tppt) cc_final: 0.8528 (tppt) REVERT: A 318 GLU cc_start: 0.8792 (pt0) cc_final: 0.8449 (pt0) REVERT: B 148 CYS cc_start: 0.7838 (t) cc_final: 0.7392 (t) REVERT: B 172 GLU cc_start: 0.6397 (mp0) cc_final: 0.6127 (mp0) REVERT: B 212 ASP cc_start: 0.8553 (t0) cc_final: 0.8353 (t0) REVERT: G 55 LYS cc_start: 0.8559 (tttp) cc_final: 0.7956 (mmtt) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1908 time to fit residues: 51.0053 Evaluate side-chains 168 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 270 GLN A 269 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7092 Z= 0.360 Angle : 0.720 10.142 9611 Z= 0.379 Chirality : 0.046 0.182 1112 Planarity : 0.005 0.085 1206 Dihedral : 5.833 56.033 955 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.18 % Rotamer: Outliers : 0.13 % Allowed : 6.99 % Favored : 92.88 % 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: -2.06 (0.27), residues: 870 helix: -0.04 (0.25), residues: 372 sheet: -2.08 (0.37), residues: 170 loop : -2.45 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.006 0.001 HIS B 62 PHE 0.029 0.002 PHE B 234 TYR 0.015 0.002 TYR B 59 ARG 0.004 0.001 ARG B 251 *********************** 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 199 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: C 164 SER cc_start: 0.8967 (t) cc_final: 0.8723 (t) REVERT: C 310 LEU cc_start: 0.7264 (mp) cc_final: 0.7027 (mp) REVERT: C 350 PHE cc_start: 0.8215 (t80) cc_final: 0.7886 (t80) REVERT: A 24 ARG cc_start: 0.5833 (mtt180) cc_final: 0.5320 (mtp-110) REVERT: A 318 GLU cc_start: 0.8983 (pt0) cc_final: 0.8589 (pt0) REVERT: B 148 CYS cc_start: 0.8035 (t) cc_final: 0.7635 (t) REVERT: B 172 GLU cc_start: 0.6481 (mp0) cc_final: 0.6236 (mp0) REVERT: B 190 LEU cc_start: 0.9253 (tt) cc_final: 0.8951 (tt) REVERT: B 212 ASP cc_start: 0.8513 (t0) cc_final: 0.8191 (t0) REVERT: B 264 TYR cc_start: 0.8202 (m-80) cc_final: 0.7695 (m-80) REVERT: B 340 ASN cc_start: 0.7922 (t0) cc_final: 0.7683 (t0) REVERT: G 55 LYS cc_start: 0.8631 (tttp) cc_final: 0.8041 (mmtt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.2035 time to fit residues: 52.6873 Evaluate side-chains 164 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 365 ASN A 331 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7092 Z= 0.191 Angle : 0.639 9.115 9611 Z= 0.328 Chirality : 0.044 0.173 1112 Planarity : 0.004 0.079 1206 Dihedral : 5.357 54.342 955 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.51 % 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: -1.63 (0.28), residues: 870 helix: 0.41 (0.26), residues: 372 sheet: -1.93 (0.37), residues: 168 loop : -2.31 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.005 0.001 HIS C 133 PHE 0.022 0.002 PHE A 199 TYR 0.017 0.001 TYR B 124 ARG 0.007 0.000 ARG C 327 *********************** 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 197 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: C 164 SER cc_start: 0.8939 (t) cc_final: 0.8713 (t) REVERT: C 235 LYS cc_start: 0.5386 (tttt) cc_final: 0.5152 (tptm) REVERT: A 24 ARG cc_start: 0.5770 (mtt180) cc_final: 0.5238 (mtp-110) REVERT: A 318 GLU cc_start: 0.8706 (pt0) cc_final: 0.8481 (pt0) REVERT: B 148 CYS cc_start: 0.7993 (t) cc_final: 0.7545 (t) REVERT: B 251 ARG cc_start: 0.7164 (mtt-85) cc_final: 0.6544 (mmm-85) REVERT: B 264 TYR cc_start: 0.7859 (m-80) cc_final: 0.7496 (m-80) REVERT: B 340 ASN cc_start: 0.7679 (t0) cc_final: 0.7369 (t0) REVERT: G 55 LYS cc_start: 0.8560 (tttp) cc_final: 0.7983 (mmtt) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2044 time to fit residues: 52.2136 Evaluate side-chains 163 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7092 Z= 0.269 Angle : 0.673 8.334 9611 Z= 0.351 Chirality : 0.045 0.173 1112 Planarity : 0.005 0.079 1206 Dihedral : 5.485 53.413 955 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.36 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -1.46 (0.28), residues: 870 helix: 0.51 (0.26), residues: 375 sheet: -1.79 (0.39), residues: 169 loop : -2.22 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 297 HIS 0.005 0.001 HIS C 133 PHE 0.018 0.002 PHE B 235 TYR 0.014 0.002 TYR B 59 ARG 0.004 0.000 ARG A 242 *********************** 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 194 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8902 (t) cc_final: 0.8688 (t) REVERT: C 355 ASN cc_start: 0.8632 (t0) cc_final: 0.8377 (t0) REVERT: A 24 ARG cc_start: 0.5813 (mtt180) cc_final: 0.5298 (mtp-110) REVERT: A 189 PHE cc_start: 0.8463 (p90) cc_final: 0.8232 (p90) REVERT: A 318 GLU cc_start: 0.8818 (pt0) cc_final: 0.8540 (pt0) REVERT: A 321 THR cc_start: 0.8814 (t) cc_final: 0.8395 (t) REVERT: B 148 CYS cc_start: 0.7823 (t) cc_final: 0.7463 (t) REVERT: B 220 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6686 (mm110) REVERT: B 340 ASN cc_start: 0.7681 (t0) cc_final: 0.7434 (t0) REVERT: G 55 LYS cc_start: 0.8575 (tttp) cc_final: 0.7993 (mmtt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2002 time to fit residues: 50.7798 Evaluate side-chains 160 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7092 Z= 0.191 Angle : 0.619 7.537 9611 Z= 0.322 Chirality : 0.043 0.173 1112 Planarity : 0.004 0.077 1206 Dihedral : 5.319 62.437 955 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 0.13 % Allowed : 2.64 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.28), residues: 870 helix: 0.72 (0.26), residues: 368 sheet: -1.69 (0.39), residues: 174 loop : -1.96 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.004 0.001 HIS C 133 PHE 0.015 0.002 PHE A 189 TYR 0.014 0.001 TYR B 264 ARG 0.008 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 198 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8880 (t) cc_final: 0.8622 (t) REVERT: C 355 ASN cc_start: 0.8572 (t0) cc_final: 0.8295 (t0) REVERT: A 24 ARG cc_start: 0.5758 (mtt180) cc_final: 0.5247 (mtp-110) REVERT: A 312 LYS cc_start: 0.8539 (mttt) cc_final: 0.8318 (mttp) REVERT: A 318 GLU cc_start: 0.8711 (pt0) cc_final: 0.8388 (pt0) REVERT: B 148 CYS cc_start: 0.7798 (t) cc_final: 0.7399 (t) REVERT: B 251 ARG cc_start: 0.6998 (mtt-85) cc_final: 0.6398 (mmm-85) REVERT: B 264 TYR cc_start: 0.7854 (m-80) cc_final: 0.7628 (m-80) REVERT: B 340 ASN cc_start: 0.7979 (t0) cc_final: 0.7777 (t0) REVERT: G 50 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7060 (mm-30) REVERT: G 55 LYS cc_start: 0.8564 (tttp) cc_final: 0.7979 (mmtt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.2106 time to fit residues: 53.7519 Evaluate side-chains 165 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 0.0970 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 301 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 255 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7092 Z= 0.177 Angle : 0.611 7.909 9611 Z= 0.317 Chirality : 0.043 0.173 1112 Planarity : 0.004 0.076 1206 Dihedral : 5.115 62.477 955 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.28), residues: 870 helix: 0.93 (0.27), residues: 367 sheet: -1.44 (0.39), residues: 169 loop : -1.91 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 135 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.002 PHE B 199 TYR 0.013 0.001 TYR B 264 ARG 0.007 0.000 ARG C 327 *********************** 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 191 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 TRP cc_start: 0.6634 (m100) cc_final: 0.6428 (m-10) REVERT: C 164 SER cc_start: 0.8919 (t) cc_final: 0.8679 (t) REVERT: C 355 ASN cc_start: 0.8601 (t0) cc_final: 0.8146 (t0) REVERT: A 15 ARG cc_start: 0.6756 (tpm170) cc_final: 0.6519 (tpt170) REVERT: A 24 ARG cc_start: 0.5732 (mtt180) cc_final: 0.5226 (mtp-110) REVERT: A 53 MET cc_start: 0.7400 (mmt) cc_final: 0.7089 (mmt) REVERT: A 312 LYS cc_start: 0.8561 (mttt) cc_final: 0.7966 (mmtt) REVERT: B 148 CYS cc_start: 0.7551 (t) cc_final: 0.7214 (t) REVERT: B 251 ARG cc_start: 0.6930 (mtt-85) cc_final: 0.6615 (mmm-85) REVERT: B 340 ASN cc_start: 0.7806 (t0) cc_final: 0.7155 (t0) REVERT: G 50 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7114 (mm-30) REVERT: G 55 LYS cc_start: 0.8707 (tttp) cc_final: 0.8216 (mmtt) REVERT: G 61 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8221 (mmmt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2304 time to fit residues: 56.9613 Evaluate side-chains 159 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 77 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7092 Z= 0.208 Angle : 0.639 7.893 9611 Z= 0.335 Chirality : 0.044 0.174 1112 Planarity : 0.004 0.076 1206 Dihedral : 5.347 75.269 955 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.75 % Favored : 94.14 % 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: -0.98 (0.29), residues: 870 helix: 0.95 (0.26), residues: 367 sheet: -1.73 (0.37), residues: 185 loop : -1.81 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.005 0.001 HIS C 348 PHE 0.022 0.002 PHE A 189 TYR 0.013 0.001 TYR A 287 ARG 0.006 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 176 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8895 (t) cc_final: 0.8621 (t) REVERT: C 355 ASN cc_start: 0.8540 (t0) cc_final: 0.8302 (t0) REVERT: A 24 ARG cc_start: 0.5752 (mtt180) cc_final: 0.5242 (mtp-110) REVERT: A 214 CYS cc_start: 0.8305 (m) cc_final: 0.8092 (m) REVERT: A 312 LYS cc_start: 0.8547 (mttt) cc_final: 0.8045 (mmtt) REVERT: B 148 CYS cc_start: 0.7792 (t) cc_final: 0.7450 (t) REVERT: G 50 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7055 (mm-30) REVERT: G 55 LYS cc_start: 0.8700 (tttp) cc_final: 0.8228 (mmtt) REVERT: G 61 LYS cc_start: 0.8780 (mmmm) cc_final: 0.8252 (mmmt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2138 time to fit residues: 48.4794 Evaluate side-chains 155 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7092 Z= 0.195 Angle : 0.649 10.452 9611 Z= 0.339 Chirality : 0.045 0.241 1112 Planarity : 0.004 0.075 1206 Dihedral : 5.371 81.278 955 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.28), residues: 870 helix: 1.10 (0.26), residues: 361 sheet: -1.56 (0.38), residues: 181 loop : -1.82 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.009 0.001 HIS C 348 PHE 0.022 0.002 PHE A 189 TYR 0.021 0.001 TYR C 71 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 176 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8889 (t) cc_final: 0.8644 (t) REVERT: C 344 PHE cc_start: 0.7415 (t80) cc_final: 0.6946 (t80) REVERT: C 355 ASN cc_start: 0.8491 (t0) cc_final: 0.8230 (t0) REVERT: A 24 ARG cc_start: 0.5777 (mtt180) cc_final: 0.5229 (mtp-110) REVERT: A 214 CYS cc_start: 0.8253 (m) cc_final: 0.7982 (t) REVERT: A 321 THR cc_start: 0.8870 (t) cc_final: 0.8210 (t) REVERT: B 148 CYS cc_start: 0.7684 (t) cc_final: 0.7412 (t) REVERT: B 264 TYR cc_start: 0.7854 (m-80) cc_final: 0.7499 (m-80) REVERT: G 50 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7021 (mm-30) REVERT: G 55 LYS cc_start: 0.8689 (tttp) cc_final: 0.8195 (mmtt) REVERT: G 61 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8258 (mmmt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2076 time to fit residues: 47.2532 Evaluate side-chains 160 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 304 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7092 Z= 0.191 Angle : 0.644 10.072 9611 Z= 0.334 Chirality : 0.044 0.215 1112 Planarity : 0.004 0.074 1206 Dihedral : 5.376 84.099 955 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.28), residues: 870 helix: 0.96 (0.26), residues: 368 sheet: -1.51 (0.38), residues: 180 loop : -1.75 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.007 0.001 HIS C 348 PHE 0.032 0.002 PHE C 175 TYR 0.015 0.001 TYR C 71 ARG 0.010 0.000 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 177 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 355 ASN cc_start: 0.8476 (t0) cc_final: 0.8072 (t0) REVERT: A 24 ARG cc_start: 0.5802 (mtt180) cc_final: 0.5234 (mtp-110) REVERT: A 214 CYS cc_start: 0.8266 (m) cc_final: 0.8039 (t) REVERT: B 148 CYS cc_start: 0.7815 (t) cc_final: 0.7481 (t) REVERT: B 264 TYR cc_start: 0.7753 (m-80) cc_final: 0.7520 (m-80) REVERT: G 50 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6967 (mm-30) REVERT: G 55 LYS cc_start: 0.8714 (tttp) cc_final: 0.8193 (mmtt) REVERT: G 61 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8228 (mmmt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1980 time to fit residues: 45.8621 Evaluate side-chains 152 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 8 optimal weight: 0.0980 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 365 ASN A 241 ASN A 255 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.177286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158831 restraints weight = 8642.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157925 restraints weight = 13447.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158419 restraints weight = 12226.357| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7092 Z= 0.177 Angle : 0.636 10.267 9611 Z= 0.330 Chirality : 0.043 0.175 1112 Planarity : 0.004 0.073 1206 Dihedral : 5.366 86.847 955 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.29), residues: 870 helix: 1.21 (0.26), residues: 362 sheet: -1.39 (0.38), residues: 181 loop : -1.67 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 339 HIS 0.006 0.001 HIS C 348 PHE 0.024 0.002 PHE A 189 TYR 0.020 0.001 TYR A 287 ARG 0.010 0.000 ARG C 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1880.19 seconds wall clock time: 34 minutes 44.35 seconds (2084.35 seconds total)