Starting phenix.real_space_refine on Tue Feb 3 18:45:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qf9_53102/02_2026/9qf9_53102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qf9_53102/02_2026/9qf9_53102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qf9_53102/02_2026/9qf9_53102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qf9_53102/02_2026/9qf9_53102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qf9_53102/02_2026/9qf9_53102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qf9_53102/02_2026/9qf9_53102.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 2014 2.51 5 N 544 2.21 5 O 652 1.98 5 H 3043 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6262 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6262 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Time building chain proxies: 1.03, per 1000 atoms: 0.16 Number of scatterers: 6262 At special positions: 0 Unit cell: (62.4, 63.7, 80.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 652 8.00 N 544 7.00 C 2014 6.00 H 3043 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.35 Conformation dependent library (CDL) restraints added in 271.2 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 742 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 41.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 113 through 127 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.607A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.523A pdb=" N ASN A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 322 through 336 removed outlier: 5.398A pdb=" N ARG A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.601A pdb=" N ASN A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 264 removed outlier: 3.912A pdb=" N SER A 263 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE A 82 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ASP A 134 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 84 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 55 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 57 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 56 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 301 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 342 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 390 removed outlier: 3.734A pdb=" N ALA A 403 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 413 through 417 removed outlier: 3.555A pdb=" N GLY A 446 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR A 447 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR A 436 " --> pdb=" O THR A 447 " (cutoff:3.500A) 122 hydrogen bonds defined for protein. 321 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: 1.15 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3039 1.12 - 1.29: 561 1.29 - 1.47: 1245 1.47 - 1.64: 1480 1.64 - 1.81: 14 Bond restraints: 6339 Sorted by residual: bond pdb=" NE2 GLN A 88 " pdb="HE22 GLN A 88 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CE2 TYR A 269 " pdb=" HE2 TYR A 269 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" ND2 ASN A 418 " pdb="HD22 ASN A 418 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CZ2 TRP A 62 " pdb=" HZ2 TRP A 62 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CE1 TYR A 237 " pdb=" HE1 TYR A 237 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 6334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 9527 2.54 - 5.08: 1407 5.08 - 7.62: 406 7.62 - 10.16: 34 10.16 - 12.70: 4 Bond angle restraints: 11378 Sorted by residual: angle pdb=" CA HIS A 377 " pdb=" CB HIS A 377 " pdb=" CG HIS A 377 " ideal model delta sigma weight residual 113.80 107.90 5.90 1.00e+00 1.00e+00 3.48e+01 angle pdb=" OE1 GLN A 52 " pdb=" CD GLN A 52 " pdb=" NE2 GLN A 52 " ideal model delta sigma weight residual 122.60 117.17 5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" C PRO A 244 " pdb=" N ASP A 245 " pdb=" CA ASP A 245 " ideal model delta sigma weight residual 122.09 131.34 -9.25 1.86e+00 2.89e-01 2.47e+01 angle pdb=" OD1 ASN A 324 " pdb=" CG ASN A 324 " pdb=" ND2 ASN A 324 " ideal model delta sigma weight residual 122.60 117.69 4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" NE ARG A 209 " pdb=" CZ ARG A 209 " pdb=" NH2 ARG A 209 " ideal model delta sigma weight residual 119.20 123.36 -4.16 9.00e-01 1.23e+00 2.13e+01 ... (remaining 11373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 2587 14.94 - 29.88: 259 29.88 - 44.82: 89 44.82 - 59.76: 55 59.76 - 74.70: 25 Dihedral angle restraints: 3015 sinusoidal: 1590 harmonic: 1425 Sorted by residual: dihedral pdb=" CA ASN A 324 " pdb=" C ASN A 324 " pdb=" N VAL A 325 " pdb=" CA VAL A 325 " ideal model delta harmonic sigma weight residual 180.00 150.78 29.22 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ASN A 312 " pdb=" C ASN A 312 " pdb=" N LYS A 313 " pdb=" CA LYS A 313 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA CYS A 393 " pdb=" C CYS A 393 " pdb=" N SER A 394 " pdb=" CA SER A 394 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 3012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 279 0.076 - 0.152: 137 0.152 - 0.228: 46 0.228 - 0.303: 7 0.303 - 0.379: 2 Chirality restraints: 471 Sorted by residual: chirality pdb=" CA ASP A 61 " pdb=" N ASP A 61 " pdb=" C ASP A 61 " pdb=" CB ASP A 61 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ASN A 319 " pdb=" N ASN A 319 " pdb=" C ASN A 319 " pdb=" CB ASN A 319 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA LYS A 338 " pdb=" N LYS A 338 " pdb=" C LYS A 338 " pdb=" CB LYS A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 468 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 157 " 0.277 2.00e-02 2.50e+03 1.03e-01 4.26e+02 pdb=" CG TRP A 157 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 157 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TRP A 157 " -0.099 2.00e-02 2.50e+03 pdb=" NE1 TRP A 157 " -0.116 2.00e-02 2.50e+03 pdb=" CE2 TRP A 157 " -0.076 2.00e-02 2.50e+03 pdb=" CE3 TRP A 157 " -0.095 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 157 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 157 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 157 " 0.046 2.00e-02 2.50e+03 pdb=" HD1 TRP A 157 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 TRP A 157 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 157 " -0.136 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 157 " 0.049 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 157 " 0.043 2.00e-02 2.50e+03 pdb=" HH2 TRP A 157 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 62 " -0.068 2.00e-02 2.50e+03 7.76e-02 2.41e+02 pdb=" CG TRP A 62 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP A 62 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 62 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP A 62 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 TRP A 62 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 62 " 0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 62 " -0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 62 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP A 62 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 TRP A 62 " -0.065 2.00e-02 2.50e+03 pdb=" HE1 TRP A 62 " 0.188 2.00e-02 2.50e+03 pdb=" HE3 TRP A 62 " 0.088 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 62 " -0.038 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 62 " 0.079 2.00e-02 2.50e+03 pdb=" HH2 TRP A 62 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 237 " 0.224 2.00e-02 2.50e+03 8.91e-02 2.38e+02 pdb=" CG TYR A 237 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 237 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR A 237 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR A 237 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 237 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 237 " 0.029 2.00e-02 2.50e+03 pdb=" OH TYR A 237 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 TYR A 237 " -0.111 2.00e-02 2.50e+03 pdb=" HD2 TYR A 237 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TYR A 237 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 TYR A 237 " -0.038 2.00e-02 2.50e+03 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 571 2.18 - 2.79: 11812 2.79 - 3.39: 19303 3.39 - 4.00: 25570 4.00 - 4.60: 37488 Nonbonded interactions: 94744 Sorted by model distance: nonbonded pdb=" OD2 ASP A 430 " pdb=" HG SER A 433 " model vdw 1.581 2.450 nonbonded pdb=" HG SER A 295 " pdb=" OD1 ASP A 297 " model vdw 1.582 2.450 nonbonded pdb=" HG SER A 286 " pdb=" OE2 GLU A 291 " model vdw 1.585 2.450 nonbonded pdb=" HG SER A 285 " pdb=" OE1 GLU A 291 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLU A 304 " pdb=" HG SER A 318 " model vdw 1.606 2.450 ... (remaining 94739 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: 0.160 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 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 : 0.012 0.041 3296 Z= 0.742 Angle : 1.803 9.248 4472 Z= 1.206 Chirality : 0.096 0.379 471 Planarity : 0.017 0.200 582 Dihedral : 14.493 74.696 1165 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.99 % Favored : 92.29 % Rotamer: Outliers : 1.15 % Allowed : 4.90 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.35), residues: 415 helix: -2.11 (0.34), residues: 140 sheet: 0.18 (0.83), residues: 34 loop : -1.28 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 346 TYR 0.181 0.024 TYR A 237 PHE 0.065 0.017 PHE A 160 TRP 0.196 0.027 TRP A 157 HIS 0.008 0.003 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.01242 ( 3296) covalent geometry : angle 1.80335 ( 4472) hydrogen bonds : bond 0.13574 ( 122) hydrogen bonds : angle 8.42661 ( 321) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9352 (mt) cc_final: 0.8971 (mt) REVERT: A 131 ILE cc_start: 0.6645 (mm) cc_final: 0.6424 (mm) REVERT: A 235 TYR cc_start: 0.8811 (t80) cc_final: 0.8517 (t80) REVERT: A 326 ILE cc_start: 0.8241 (mm) cc_final: 0.8003 (tp) outliers start: 4 outliers final: 3 residues processed: 108 average time/residue: 0.1768 time to fit residues: 22.0201 Evaluate side-chains 86 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 195 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 = 0.3775 r_free = 0.3775 target = 0.102578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072115 restraints weight = 32272.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.078388 restraints weight = 18422.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.083315 restraints weight = 11961.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086906 restraints weight = 8386.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.089661 restraints weight = 6200.581| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3296 Z= 0.174 Angle : 0.657 5.858 4472 Z= 0.383 Chirality : 0.043 0.141 471 Planarity : 0.004 0.039 582 Dihedral : 7.746 29.266 447 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.36), residues: 415 helix: -1.30 (0.37), residues: 141 sheet: -0.90 (0.59), residues: 63 loop : -1.31 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 274 TYR 0.019 0.002 TYR A 258 PHE 0.016 0.003 PHE A 317 TRP 0.014 0.002 TRP A 226 HIS 0.012 0.002 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3296) covalent geometry : angle 0.65687 ( 4472) hydrogen bonds : bond 0.05003 ( 122) hydrogen bonds : angle 6.59263 ( 321) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9504 (mt) cc_final: 0.9295 (mt) REVERT: A 121 CYS cc_start: 0.8832 (m) cc_final: 0.8005 (t) REVERT: A 131 ILE cc_start: 0.8496 (mm) cc_final: 0.8224 (mm) REVERT: A 356 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8531 (mmtm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1967 time to fit residues: 20.6214 Evaluate side-chains 72 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 7.9990 chunk 36 optimal weight: 0.1980 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.104610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.072893 restraints weight = 31492.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079394 restraints weight = 18452.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.084649 restraints weight = 12127.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088621 restraints weight = 8470.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.091511 restraints weight = 6225.544| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3296 Z= 0.120 Angle : 0.534 4.481 4472 Z= 0.303 Chirality : 0.043 0.147 471 Planarity : 0.004 0.045 582 Dihedral : 6.476 24.024 447 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.37), residues: 415 helix: -0.61 (0.41), residues: 143 sheet: -1.10 (0.54), residues: 69 loop : -1.32 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.030 0.002 TYR A 422 PHE 0.009 0.002 PHE A 317 TRP 0.010 0.001 TRP A 157 HIS 0.011 0.002 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3296) covalent geometry : angle 0.53444 ( 4472) hydrogen bonds : bond 0.03834 ( 122) hydrogen bonds : angle 5.91965 ( 321) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9495 (mt) cc_final: 0.9242 (mt) REVERT: A 73 LYS cc_start: 0.9419 (mttt) cc_final: 0.8927 (tptt) REVERT: A 131 ILE cc_start: 0.8498 (mm) cc_final: 0.8172 (mm) REVERT: A 241 LEU cc_start: 0.8633 (tt) cc_final: 0.8380 (mm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2055 time to fit residues: 20.8960 Evaluate side-chains 74 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 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 = 0.3725 r_free = 0.3725 target = 0.100110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.069234 restraints weight = 32486.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075326 restraints weight = 19199.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.080282 restraints weight = 12694.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084044 restraints weight = 8883.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.086884 restraints weight = 6512.344| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3296 Z= 0.167 Angle : 0.547 4.511 4472 Z= 0.316 Chirality : 0.042 0.143 471 Planarity : 0.004 0.043 582 Dihedral : 6.301 22.241 447 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.38), residues: 415 helix: -0.74 (0.42), residues: 143 sheet: -1.24 (0.55), residues: 68 loop : -1.41 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 141 TYR 0.013 0.002 TYR A 235 PHE 0.011 0.002 PHE A 317 TRP 0.013 0.001 TRP A 302 HIS 0.010 0.002 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3296) covalent geometry : angle 0.54745 ( 4472) hydrogen bonds : bond 0.03903 ( 122) hydrogen bonds : angle 6.06695 ( 321) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2075 time to fit residues: 18.9222 Evaluate side-chains 71 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 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 = 0.3741 r_free = 0.3741 target = 0.102061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070623 restraints weight = 32693.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076710 restraints weight = 19383.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081641 restraints weight = 12885.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.085467 restraints weight = 9134.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088374 restraints weight = 6752.476| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3296 Z= 0.133 Angle : 0.523 4.609 4472 Z= 0.299 Chirality : 0.042 0.142 471 Planarity : 0.004 0.042 582 Dihedral : 6.008 22.250 447 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.39), residues: 415 helix: -0.50 (0.43), residues: 143 sheet: -1.35 (0.55), residues: 68 loop : -1.31 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.023 0.002 TYR A 422 PHE 0.009 0.001 PHE A 317 TRP 0.010 0.001 TRP A 302 HIS 0.010 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3296) covalent geometry : angle 0.52278 ( 4472) hydrogen bonds : bond 0.03669 ( 122) hydrogen bonds : angle 5.90614 ( 321) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1966 time to fit residues: 17.8789 Evaluate side-chains 69 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 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 = 0.3808 r_free = 0.3808 target = 0.106905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.073390 restraints weight = 31773.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080078 restraints weight = 18677.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.085359 restraints weight = 12343.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.089466 restraints weight = 8704.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092507 restraints weight = 6432.189| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3296 Z= 0.119 Angle : 0.497 4.252 4472 Z= 0.282 Chirality : 0.041 0.140 471 Planarity : 0.004 0.041 582 Dihedral : 5.714 20.416 447 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.39), residues: 415 helix: -0.44 (0.44), residues: 143 sheet: -1.54 (0.57), residues: 65 loop : -1.31 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 141 TYR 0.012 0.001 TYR A 96 PHE 0.009 0.001 PHE A 317 TRP 0.013 0.001 TRP A 302 HIS 0.008 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3296) covalent geometry : angle 0.49663 ( 4472) hydrogen bonds : bond 0.03260 ( 122) hydrogen bonds : angle 5.74385 ( 321) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9532 (mt) cc_final: 0.9318 (mt) REVERT: A 252 GLU cc_start: 0.9550 (mp0) cc_final: 0.9343 (pm20) REVERT: A 261 TYR cc_start: 0.8583 (m-80) cc_final: 0.8074 (m-80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2366 time to fit residues: 21.6521 Evaluate side-chains 68 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.068006 restraints weight = 32723.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074139 restraints weight = 19300.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.079192 restraints weight = 12808.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.083095 restraints weight = 9060.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.085833 restraints weight = 6699.206| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3296 Z= 0.182 Angle : 0.539 4.179 4472 Z= 0.314 Chirality : 0.041 0.141 471 Planarity : 0.004 0.041 582 Dihedral : 5.878 20.514 447 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.38), residues: 415 helix: -0.49 (0.44), residues: 136 sheet: -1.50 (0.60), residues: 58 loop : -1.50 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 398 TYR 0.015 0.002 TYR A 235 PHE 0.015 0.002 PHE A 317 TRP 0.021 0.002 TRP A 302 HIS 0.009 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3296) covalent geometry : angle 0.53892 ( 4472) hydrogen bonds : bond 0.03810 ( 122) hydrogen bonds : angle 5.93673 ( 321) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9500 (mt) cc_final: 0.9289 (mt) REVERT: A 126 LYS cc_start: 0.9527 (tmtt) cc_final: 0.9281 (tmtt) REVERT: A 252 GLU cc_start: 0.9637 (mp0) cc_final: 0.9400 (pm20) REVERT: A 261 TYR cc_start: 0.8650 (m-80) cc_final: 0.8162 (m-80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2255 time to fit residues: 20.2000 Evaluate side-chains 70 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** 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 = 0.3780 r_free = 0.3780 target = 0.105687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072144 restraints weight = 32657.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.078518 restraints weight = 19445.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.083945 restraints weight = 12954.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.088014 restraints weight = 9172.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091078 restraints weight = 6822.165| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3296 Z= 0.111 Angle : 0.488 4.212 4472 Z= 0.277 Chirality : 0.041 0.138 471 Planarity : 0.004 0.039 582 Dihedral : 5.541 20.414 447 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.39), residues: 415 helix: -0.34 (0.45), residues: 137 sheet: -1.44 (0.64), residues: 55 loop : -1.32 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 274 TYR 0.011 0.001 TYR A 96 PHE 0.014 0.001 PHE A 317 TRP 0.011 0.001 TRP A 302 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3296) covalent geometry : angle 0.48826 ( 4472) hydrogen bonds : bond 0.03162 ( 122) hydrogen bonds : angle 5.61414 ( 321) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9545 (mt) cc_final: 0.9313 (mt) REVERT: A 126 LYS cc_start: 0.9502 (tmtt) cc_final: 0.9249 (tmtt) REVERT: A 188 TYR cc_start: 0.9292 (t80) cc_final: 0.8914 (t80) REVERT: A 261 TYR cc_start: 0.8691 (m-80) cc_final: 0.8193 (m-80) REVERT: A 374 ASN cc_start: 0.8705 (m-40) cc_final: 0.8393 (m-40) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2166 time to fit residues: 19.1188 Evaluate side-chains 71 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.103021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070445 restraints weight = 32732.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076710 restraints weight = 19504.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081877 restraints weight = 13018.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085819 restraints weight = 9228.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.088790 restraints weight = 6842.273| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3296 Z= 0.136 Angle : 0.491 4.182 4472 Z= 0.282 Chirality : 0.041 0.139 471 Planarity : 0.004 0.039 582 Dihedral : 5.525 19.828 447 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.39), residues: 415 helix: -0.24 (0.45), residues: 134 sheet: -1.41 (0.57), residues: 66 loop : -1.28 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 274 TYR 0.012 0.001 TYR A 96 PHE 0.014 0.002 PHE A 317 TRP 0.017 0.001 TRP A 302 HIS 0.008 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3296) covalent geometry : angle 0.49106 ( 4472) hydrogen bonds : bond 0.03286 ( 122) hydrogen bonds : angle 5.65370 ( 321) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9548 (mt) cc_final: 0.9324 (mt) REVERT: A 126 LYS cc_start: 0.9523 (tmtt) cc_final: 0.9277 (tmtt) REVERT: A 188 TYR cc_start: 0.9310 (t80) cc_final: 0.8877 (t80) REVERT: A 261 TYR cc_start: 0.8724 (m-80) cc_final: 0.8223 (m-80) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2432 time to fit residues: 21.2325 Evaluate side-chains 70 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 337 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 = 0.3777 r_free = 0.3777 target = 0.102957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.069876 restraints weight = 32615.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076379 restraints weight = 19531.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.081745 restraints weight = 12969.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.085797 restraints weight = 9179.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.088868 restraints weight = 6787.700| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3296 Z= 0.115 Angle : 0.484 4.191 4472 Z= 0.275 Chirality : 0.041 0.139 471 Planarity : 0.004 0.038 582 Dihedral : 5.448 19.705 447 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.40), residues: 415 helix: -0.22 (0.45), residues: 136 sheet: -1.27 (0.61), residues: 61 loop : -1.27 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 274 TYR 0.011 0.001 TYR A 96 PHE 0.019 0.002 PHE A 79 TRP 0.013 0.001 TRP A 302 HIS 0.006 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3296) covalent geometry : angle 0.48434 ( 4472) hydrogen bonds : bond 0.03068 ( 122) hydrogen bonds : angle 5.54480 ( 321) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9547 (mt) cc_final: 0.9319 (mt) REVERT: A 126 LYS cc_start: 0.9519 (tmtt) cc_final: 0.9293 (tmtt) REVERT: A 184 THR cc_start: 0.8472 (m) cc_final: 0.8155 (p) REVERT: A 188 TYR cc_start: 0.9302 (t80) cc_final: 0.8832 (t80) REVERT: A 261 TYR cc_start: 0.8755 (m-80) cc_final: 0.8268 (m-80) REVERT: A 374 ASN cc_start: 0.8082 (m-40) cc_final: 0.7848 (m-40) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2091 time to fit residues: 18.5217 Evaluate side-chains 74 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 0.0370 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 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 = 0.3782 r_free = 0.3782 target = 0.104417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071094 restraints weight = 32330.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.077432 restraints weight = 19163.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082862 restraints weight = 12764.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.086899 restraints weight = 8999.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089928 restraints weight = 6659.594| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3296 Z= 0.120 Angle : 0.477 4.141 4472 Z= 0.271 Chirality : 0.041 0.136 471 Planarity : 0.004 0.038 582 Dihedral : 5.346 19.229 447 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.40), residues: 415 helix: -0.11 (0.45), residues: 134 sheet: -1.23 (0.61), residues: 61 loop : -1.17 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 274 TYR 0.011 0.001 TYR A 96 PHE 0.015 0.002 PHE A 79 TRP 0.015 0.001 TRP A 302 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3296) covalent geometry : angle 0.47711 ( 4472) hydrogen bonds : bond 0.03050 ( 122) hydrogen bonds : angle 5.51903 ( 321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.28 seconds wall clock time: 30 minutes 8.43 seconds (1808.43 seconds total)