Starting phenix.real_space_refine on Wed Feb 12 00:05:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l0p_23099/02_2025/7l0p_23099.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l0p_23099/02_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_23099/02_2025/7l0p_23099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l0p_23099/02_2025/7l0p_23099.map" model { file = "/net/cci-nas-00/data/ceres_data/7l0p_23099/02_2025/7l0p_23099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l0p_23099/02_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-5592/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: 4.48, 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: 1.63 Conformation dependent library (CDL) restraints added in 1.1 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: 0.69 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: 1.91 Time building geometry restraints manager: 1.94 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.610 Find NCS groups from input model: 0.070 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- 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 : 0.802 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: 0.2265 time to fit residues: 65.1795 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 : 0.731 ------------------------------------------------------------------------------- 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 = 10280.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144052 restraints weight = 9811.461| |-----------------------------------------------------------------------------| 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 : 0.746 Fit side-chains revert: symmetry clash REVERT: C 350 PHE cc_start: 0.7999 (t80) cc_final: 0.7769 (t80) REVERT: A 18 MET cc_start: 0.7095 (tpp) cc_final: 0.6820 (ttt) REVERT: A 24 ARG cc_start: 0.6162 (mtt180) cc_final: 0.5687 (mtp-110) REVERT: A 248 LYS cc_start: 0.8528 (tppt) cc_final: 0.8286 (tppt) REVERT: A 304 GLN cc_start: 0.8135 (tt0) cc_final: 0.7737 (tt0) REVERT: B 251 ARG cc_start: 0.7138 (mtt-85) cc_final: 0.6852 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.1995 time to fit residues: 53.3011 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 : 0.764 ------------------------------------------------------------------------------- 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: 2.9990 chunk 81 optimal weight: 0.0040 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.174124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156028 restraints weight = 8860.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154242 restraints weight = 14174.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154837 restraints weight = 13987.949| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2610 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= 0.188 Angle : 0.622 7.341 9611 Z= 0.325 Chirality : 0.043 0.176 1112 Planarity : 0.005 0.079 1206 Dihedral : 5.409 59.417 955 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.86 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -1.88 (0.27), residues: 870 helix: 0.01 (0.25), residues: 379 sheet: -1.81 (0.36), residues: 169 loop : -2.38 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 339 HIS 0.005 0.001 HIS C 133 PHE 0.024 0.002 PHE B 234 TYR 0.017 0.001 TYR B 264 ARG 0.005 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 201 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8722 (t) cc_final: 0.8459 (t) REVERT: A 24 ARG cc_start: 0.6218 (mtt180) cc_final: 0.5971 (mtp-110) REVERT: A 248 LYS cc_start: 0.8390 (tppt) cc_final: 0.8189 (tppt) REVERT: A 287 TYR cc_start: 0.7091 (m-80) cc_final: 0.6803 (m-10) REVERT: A 304 GLN cc_start: 0.7951 (tt0) cc_final: 0.7646 (tt0) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2534 time to fit residues: 66.5036 Evaluate side-chains 168 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.176026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158730 restraints weight = 8731.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157621 restraints weight = 13891.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.157907 restraints weight = 12672.983| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3034 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= 0.182 Angle : 0.617 7.543 9611 Z= 0.323 Chirality : 0.043 0.171 1112 Planarity : 0.004 0.077 1206 Dihedral : 5.192 57.396 955 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.94 % Rotamer: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.17 % 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: -1.57 (0.27), residues: 870 helix: 0.41 (0.26), residues: 377 sheet: -1.77 (0.36), residues: 173 loop : -2.33 (0.31), residues: 320 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 0.018 0.001 PHE B 234 TYR 0.009 0.001 TYR B 264 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 196 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: C 164 SER cc_start: 0.8710 (t) cc_final: 0.8416 (t) REVERT: C 235 LYS cc_start: 0.5621 (tttt) cc_final: 0.5392 (tptm) REVERT: A 24 ARG cc_start: 0.6299 (mtt180) cc_final: 0.5950 (mtp-110) REVERT: A 214 CYS cc_start: 0.7973 (m) cc_final: 0.7683 (t) REVERT: A 248 LYS cc_start: 0.8382 (tppt) cc_final: 0.8097 (tppt) REVERT: A 312 LYS cc_start: 0.8109 (mttt) cc_final: 0.7704 (mmtt) REVERT: B 264 TYR cc_start: 0.7494 (m-80) cc_final: 0.7212 (m-80) REVERT: B 284 LEU cc_start: 0.8231 (tt) cc_final: 0.8026 (tt) REVERT: G 67 LEU cc_start: 0.8007 (mm) cc_final: 0.7771 (mm) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2195 time to fit residues: 55.0026 Evaluate side-chains 160 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141953 restraints weight = 8803.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143186 restraints weight = 7190.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143586 restraints weight = 6167.774| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3215 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= 0.222 Angle : 0.647 7.924 9611 Z= 0.339 Chirality : 0.045 0.173 1112 Planarity : 0.005 0.077 1206 Dihedral : 5.246 56.896 955 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.27), residues: 870 helix: 0.48 (0.26), residues: 378 sheet: -1.57 (0.39), residues: 166 loop : -2.27 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS C 133 PHE 0.021 0.002 PHE B 199 TYR 0.023 0.002 TYR C 324 ARG 0.007 0.000 ARG C 328 *********************** 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 192 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: C 164 SER cc_start: 0.8829 (t) cc_final: 0.8561 (t) REVERT: C 350 PHE cc_start: 0.8040 (t80) cc_final: 0.7767 (t80) REVERT: A 24 ARG cc_start: 0.6055 (mtt180) cc_final: 0.5726 (mtp-110) REVERT: A 53 MET cc_start: 0.7326 (mmt) cc_final: 0.7112 (mmt) REVERT: A 198 MET cc_start: 0.8209 (ttm) cc_final: 0.7855 (ttm) REVERT: A 312 LYS cc_start: 0.8323 (mttt) cc_final: 0.7801 (mmtt) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2092 time to fit residues: 52.4480 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 : 0.703 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 47 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 ASN A 52 GLN A 188 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158937 restraints weight = 8724.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.157635 restraints weight = 12588.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156295 restraints weight = 12309.375| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3572 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= 0.170 Angle : 0.618 8.404 9611 Z= 0.321 Chirality : 0.043 0.174 1112 Planarity : 0.004 0.074 1206 Dihedral : 5.002 56.046 955 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.29 % Favored : 94.60 % Rotamer: Outliers : 0.13 % Allowed : 2.37 % Favored : 97.49 % 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: -1.20 (0.28), residues: 870 helix: 0.67 (0.26), residues: 378 sheet: -1.48 (0.39), residues: 166 loop : -2.14 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 339 HIS 0.004 0.001 HIS C 133 PHE 0.021 0.001 PHE A 189 TYR 0.016 0.001 TYR C 324 ARG 0.007 0.001 ARG A 242 *********************** 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 202 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: C 164 SER cc_start: 0.8693 (t) cc_final: 0.8419 (t) REVERT: A 24 ARG cc_start: 0.6261 (mtt180) cc_final: 0.5935 (mtp-110) REVERT: A 53 MET cc_start: 0.6936 (mmt) cc_final: 0.6650 (mmt) REVERT: A 214 CYS cc_start: 0.7834 (m) cc_final: 0.7613 (t) REVERT: A 312 LYS cc_start: 0.8122 (mttt) cc_final: 0.7791 (mmtt) REVERT: A 321 THR cc_start: 0.8992 (t) cc_final: 0.8402 (t) REVERT: G 67 LEU cc_start: 0.8058 (mm) cc_final: 0.7855 (mm) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2342 time to fit residues: 60.9236 Evaluate side-chains 158 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.172941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154141 restraints weight = 8714.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151197 restraints weight = 14761.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152005 restraints weight = 14626.688| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3658 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= 0.221 Angle : 0.651 8.231 9611 Z= 0.339 Chirality : 0.045 0.174 1112 Planarity : 0.004 0.074 1206 Dihedral : 5.517 84.190 955 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.28), residues: 870 helix: 0.79 (0.26), residues: 372 sheet: -1.38 (0.40), residues: 166 loop : -2.03 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 297 HIS 0.004 0.001 HIS C 133 PHE 0.025 0.002 PHE B 234 TYR 0.017 0.002 TYR C 324 ARG 0.007 0.000 ARG C 328 *********************** 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 195 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8800 (t) cc_final: 0.8534 (t) REVERT: A 24 ARG cc_start: 0.6253 (mtt180) cc_final: 0.5943 (mtp-110) REVERT: A 312 LYS cc_start: 0.8259 (mttt) cc_final: 0.7905 (mmtt) REVERT: A 321 THR cc_start: 0.8952 (t) cc_final: 0.8203 (t) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2245 time to fit residues: 56.0513 Evaluate side-chains 156 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 0.7980 chunk 70 optimal weight: 0.9990 chunk 82 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 365 ASN A 304 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.177421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158822 restraints weight = 8705.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156528 restraints weight = 14877.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155460 restraints weight = 14208.223| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7092 Z= 0.172 Angle : 0.622 8.558 9611 Z= 0.325 Chirality : 0.044 0.217 1112 Planarity : 0.004 0.072 1206 Dihedral : 5.130 73.712 955 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.90 (0.28), residues: 870 helix: 0.97 (0.26), residues: 366 sheet: -1.31 (0.39), residues: 166 loop : -1.97 (0.31), residues: 338 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 0.015 0.002 PHE A 189 TYR 0.018 0.001 TYR C 324 ARG 0.004 0.000 ARG B 219 *********************** 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 185 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8787 (t) cc_final: 0.8582 (t) REVERT: C 310 LEU cc_start: 0.7226 (mp) cc_final: 0.6905 (mp) REVERT: A 24 ARG cc_start: 0.6202 (mtt180) cc_final: 0.5834 (mtp-110) REVERT: A 312 LYS cc_start: 0.8259 (mttt) cc_final: 0.7929 (mmtt) REVERT: B 251 ARG cc_start: 0.7265 (mtt-85) cc_final: 0.6886 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2270 time to fit residues: 55.3554 Evaluate side-chains 155 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN ** 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 = 0.4000 r_free = 0.4000 target = 0.177357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.158479 restraints weight = 8775.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157332 restraints weight = 12627.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155374 restraints weight = 12009.463| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3981 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= 0.205 Angle : 0.648 8.523 9611 Z= 0.340 Chirality : 0.045 0.171 1112 Planarity : 0.004 0.071 1206 Dihedral : 5.172 71.734 955 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.88 (0.28), residues: 870 helix: 0.94 (0.26), residues: 366 sheet: -1.27 (0.39), residues: 173 loop : -1.91 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 297 HIS 0.005 0.001 HIS C 348 PHE 0.023 0.002 PHE C 344 TYR 0.019 0.002 TYR C 154 ARG 0.004 0.000 ARG B 219 *********************** 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 180 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8849 (t) cc_final: 0.8587 (t) REVERT: A 24 ARG cc_start: 0.6199 (mtt180) cc_final: 0.5838 (mtp-110) REVERT: A 312 LYS cc_start: 0.8276 (mttt) cc_final: 0.7941 (mmtt) REVERT: B 190 LEU cc_start: 0.9225 (tt) cc_final: 0.8936 (tt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2077 time to fit residues: 48.5807 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 : 0.790 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 365 ASN A 213 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.175264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156828 restraints weight = 9016.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155136 restraints weight = 16009.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155468 restraints weight = 14154.274| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7092 Z= 0.229 Angle : 0.670 8.495 9611 Z= 0.354 Chirality : 0.046 0.213 1112 Planarity : 0.005 0.073 1206 Dihedral : 5.494 87.069 955 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.79 % 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: -0.89 (0.28), residues: 870 helix: 0.94 (0.26), residues: 362 sheet: -1.49 (0.38), residues: 183 loop : -1.74 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 297 HIS 0.006 0.001 HIS C 348 PHE 0.025 0.002 PHE C 344 TYR 0.016 0.002 TYR C 324 ARG 0.005 0.000 ARG B 219 ********************** 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 174 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 SER cc_start: 0.8695 (t) cc_final: 0.8436 (t) REVERT: C 238 ILE cc_start: 0.7478 (mm) cc_final: 0.7236 (mm) REVERT: C 310 LEU cc_start: 0.7035 (mp) cc_final: 0.6785 (mp) REVERT: A 24 ARG cc_start: 0.6267 (mtt180) cc_final: 0.5967 (mtp-110) REVERT: A 312 LYS cc_start: 0.8209 (mttt) cc_final: 0.7936 (mmtt) REVERT: G 67 LEU cc_start: 0.8164 (mm) cc_final: 0.7945 (mm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2127 time to fit residues: 47.9622 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 : 0.793 ------------------------------------------------------------------------------- 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: 30.0000 chunk 13 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157781 restraints weight = 8852.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156465 restraints weight = 14288.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155437 restraints weight = 13273.113| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4068 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= 0.210 Angle : 0.664 8.417 9611 Z= 0.349 Chirality : 0.045 0.205 1112 Planarity : 0.004 0.074 1206 Dihedral : 5.368 81.696 955 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.48 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % 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: -0.77 (0.28), residues: 870 helix: 1.00 (0.26), residues: 362 sheet: -1.25 (0.39), residues: 178 loop : -1.74 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 297 HIS 0.004 0.001 HIS C 133 PHE 0.017 0.002 PHE B 253 TYR 0.016 0.002 TYR C 324 ARG 0.004 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.56 seconds wall clock time: 44 minutes 39.20 seconds (2679.20 seconds total)