Starting phenix.real_space_refine on Fri Aug 22 13:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r68_18948/08_2025/8r68_18948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r68_18948/08_2025/8r68_18948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r68_18948/08_2025/8r68_18948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r68_18948/08_2025/8r68_18948.map" model { file = "/net/cci-nas-00/data/ceres_data/8r68_18948/08_2025/8r68_18948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r68_18948/08_2025/8r68_18948.cif" } resolution = 3.6 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= -0.000 sd= 0.055 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 14 5.16 5 C 2082 2.51 5 N 579 2.21 5 O 566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3241 Classifications: {'peptide': 391} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 374} Chain breaks: 6 Time building chain proxies: 1.03, per 1000 atoms: 0.32 Number of scatterers: 3241 At special positions: 0 Unit cell: (53.248, 59.904, 112.32, 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 14 16.00 O 566 8.00 N 579 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.19 Conformation dependent library (CDL) restraints added in 85.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 49.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 60 through 65 removed outlier: 4.277A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.570A pdb=" N ASN A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.513A pdb=" N SER A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.890A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.819A pdb=" N ARG A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.658A pdb=" N GLU A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.691A pdb=" N PHE A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.542A pdb=" N SER A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 4.197A pdb=" N ASP A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 261 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.685A pdb=" N ALA A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N MET A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.528A pdb=" N PHE A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 removed outlier: 4.150A pdb=" N TYR A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A 342 " --> pdb=" O TYR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.758A pdb=" N TRP A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 359' Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.545A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 Processing sheet with id=AA1, first strand: chain 'A' and resid 424 through 426 removed outlier: 8.932A pdb=" N SER A 377 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 351 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU A 379 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 408 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 441 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 439 " --> pdb=" O ALA A 410 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 285 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: 0.32 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1044 1.34 - 1.45: 508 1.45 - 1.57: 1750 1.57 - 1.69: 0 1.69 - 1.80: 25 Bond restraints: 3327 Sorted by residual: bond pdb=" CA TRP A 312 " pdb=" CB TRP A 312 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.38e-02 5.25e+03 8.67e-01 bond pdb=" CB ARG A 105 " pdb=" CG ARG A 105 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.39e-01 bond pdb=" CA ASP A 232 " pdb=" C ASP A 232 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.62e-01 bond pdb=" CB ASP A 386 " pdb=" CG ASP A 386 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.35e-01 bond pdb=" C ASP A 232 " pdb=" N PRO A 233 " ideal model delta sigma weight residual 1.334 1.352 -0.019 2.34e-02 1.83e+03 6.27e-01 ... (remaining 3322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 4275 1.25 - 2.49: 161 2.49 - 3.74: 40 3.74 - 4.98: 14 4.98 - 6.23: 5 Bond angle restraints: 4495 Sorted by residual: angle pdb=" N GLY A 311 " pdb=" CA GLY A 311 " pdb=" C GLY A 311 " ideal model delta sigma weight residual 115.31 111.52 3.79 1.24e+00 6.50e-01 9.36e+00 angle pdb=" CA ARG A 105 " pdb=" CB ARG A 105 " pdb=" CG ARG A 105 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.63e+00 angle pdb=" CA GLN A 234 " pdb=" CB GLN A 234 " pdb=" CG GLN A 234 " ideal model delta sigma weight residual 114.10 118.98 -4.88 2.00e+00 2.50e-01 5.96e+00 angle pdb=" N ASP A 271 " pdb=" CA ASP A 271 " pdb=" C ASP A 271 " ideal model delta sigma weight residual 110.44 113.34 -2.90 1.20e+00 6.94e-01 5.85e+00 angle pdb=" CA GLU A 448 " pdb=" CB GLU A 448 " pdb=" CG GLU A 448 " ideal model delta sigma weight residual 114.10 118.45 -4.35 2.00e+00 2.50e-01 4.73e+00 ... (remaining 4490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 1749 14.15 - 28.30: 139 28.30 - 42.45: 47 42.45 - 56.60: 11 56.60 - 70.75: 7 Dihedral angle restraints: 1953 sinusoidal: 816 harmonic: 1137 Sorted by residual: dihedral pdb=" CA ASP A 232 " pdb=" C ASP A 232 " pdb=" N PRO A 233 " pdb=" CA PRO A 233 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA TRP A 312 " pdb=" C TRP A 312 " pdb=" N LEU A 313 " pdb=" CA LEU A 313 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN A 86 " pdb=" CB ASN A 86 " pdb=" CG ASN A 86 " pdb=" OD1 ASN A 86 " ideal model delta sinusoidal sigma weight residual 120.00 -173.52 -66.48 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 1950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 281 0.034 - 0.067: 136 0.067 - 0.100: 35 0.100 - 0.134: 8 0.134 - 0.167: 2 Chirality restraints: 462 Sorted by residual: chirality pdb=" CB ILE A 393 " pdb=" CA ILE A 393 " pdb=" CG1 ILE A 393 " pdb=" CG2 ILE A 393 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA VAL A 390 " pdb=" N VAL A 390 " pdb=" C VAL A 390 " pdb=" CB VAL A 390 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 209 " pdb=" N ILE A 209 " pdb=" C ILE A 209 " pdb=" CB ILE A 209 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 459 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 232 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO A 233 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 444 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 445 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 358 " -0.014 2.00e-02 2.50e+03 1.11e-02 3.10e+00 pdb=" CG TRP A 358 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 358 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 358 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 358 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 358 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 358 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 358 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 358 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 358 " -0.004 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 551 2.76 - 3.30: 3237 3.30 - 3.83: 5264 3.83 - 4.37: 6481 4.37 - 4.90: 10254 Nonbonded interactions: 25787 Sorted by model distance: nonbonded pdb=" NH1 ARG A 113 " pdb=" OD2 ASP A 123 " model vdw 2.228 3.120 nonbonded pdb=" OD2 ASP A 317 " pdb=" OG1 THR A 349 " model vdw 2.248 3.040 nonbonded pdb=" O LEU A 313 " pdb=" OG1 THR A 349 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 247 " pdb=" NH2 ARG A 253 " model vdw 2.260 3.120 nonbonded pdb=" O ASP A 254 " pdb=" OG1 THR A 258 " model vdw 2.280 3.040 ... (remaining 25782 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.280 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5279 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 : 0.003 0.027 3327 Z= 0.132 Angle : 0.648 6.230 4495 Z= 0.345 Chirality : 0.041 0.167 462 Planarity : 0.006 0.071 573 Dihedral : 13.088 70.751 1217 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.30 % Allowed : 0.89 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -1.70 (0.43), residues: 377 helix: -1.79 (0.42), residues: 128 sheet: 0.61 (0.79), residues: 38 loop : -0.97 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 454 TYR 0.009 0.001 TYR A 156 PHE 0.010 0.001 PHE A 342 TRP 0.029 0.002 TRP A 358 HIS 0.003 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3327) covalent geometry : angle 0.64843 ( 4495) hydrogen bonds : bond 0.31931 ( 101) hydrogen bonds : angle 10.47196 ( 285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7504 (m-10) cc_final: 0.6708 (m-80) REVERT: A 384 ASN cc_start: 0.8229 (m-40) cc_final: 0.7990 (m-40) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.0669 time to fit residues: 5.9438 Evaluate side-chains 61 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.280812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.243052 restraints weight = 4565.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.250881 restraints weight = 2685.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.255809 restraints weight = 1813.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.258720 restraints weight = 1365.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.260345 restraints weight = 1127.410| |-----------------------------------------------------------------------------| r_work (final): 0.4938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5252 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3327 Z= 0.151 Angle : 0.682 8.132 4495 Z= 0.346 Chirality : 0.044 0.143 462 Planarity : 0.006 0.064 573 Dihedral : 5.390 28.435 434 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.89 % Allowed : 7.44 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -1.84 (0.41), residues: 377 helix: -1.62 (0.40), residues: 137 sheet: 0.40 (0.87), residues: 32 loop : -1.14 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 454 TYR 0.016 0.002 TYR A 90 PHE 0.023 0.002 PHE A 368 TRP 0.051 0.003 TRP A 312 HIS 0.002 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3327) covalent geometry : angle 0.68191 ( 4495) hydrogen bonds : bond 0.05470 ( 101) hydrogen bonds : angle 6.99036 ( 285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7329 (m-10) cc_final: 0.6585 (m-80) outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.0689 time to fit residues: 5.7189 Evaluate side-chains 64 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.0050 chunk 29 optimal weight: 0.0270 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.283848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.248152 restraints weight = 4622.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.255519 restraints weight = 2646.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.260030 restraints weight = 1782.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.262526 restraints weight = 1351.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.264703 restraints weight = 1125.371| |-----------------------------------------------------------------------------| r_work (final): 0.4960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5117 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3327 Z= 0.122 Angle : 0.596 6.396 4495 Z= 0.304 Chirality : 0.043 0.143 462 Planarity : 0.005 0.059 573 Dihedral : 5.134 28.052 434 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.89 % Allowed : 10.71 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -1.84 (0.42), residues: 377 helix: -1.45 (0.40), residues: 148 sheet: -0.14 (0.81), residues: 38 loop : -1.16 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.014 0.001 TYR A 90 PHE 0.027 0.001 PHE A 368 TRP 0.032 0.002 TRP A 312 HIS 0.004 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3327) covalent geometry : angle 0.59624 ( 4495) hydrogen bonds : bond 0.04402 ( 101) hydrogen bonds : angle 6.28231 ( 285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7258 (m-10) cc_final: 0.6524 (m-80) REVERT: A 272 GLN cc_start: 0.6455 (mt0) cc_final: 0.5909 (mt0) outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.0666 time to fit residues: 6.0187 Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 223 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.0010 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.277127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.240673 restraints weight = 4390.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.248062 restraints weight = 2471.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.252428 restraints weight = 1655.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.255461 restraints weight = 1251.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.257022 restraints weight = 1027.174| |-----------------------------------------------------------------------------| r_work (final): 0.4900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3327 Z= 0.166 Angle : 0.664 7.676 4495 Z= 0.333 Chirality : 0.048 0.271 462 Planarity : 0.005 0.056 573 Dihedral : 5.496 27.285 434 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.49 % Allowed : 14.29 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -2.20 (0.41), residues: 377 helix: -1.81 (0.38), residues: 158 sheet: -0.45 (0.90), residues: 32 loop : -1.21 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.012 0.002 TYR A 462 PHE 0.026 0.002 PHE A 368 TRP 0.014 0.002 TRP A 312 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 3327) covalent geometry : angle 0.66416 ( 4495) hydrogen bonds : bond 0.04532 ( 101) hydrogen bonds : angle 6.53914 ( 285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.7352 (m-10) cc_final: 0.6584 (m-80) REVERT: A 248 GLN cc_start: 0.6330 (pm20) cc_final: 0.6066 (tt0) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.0729 time to fit residues: 6.4040 Evaluate side-chains 67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.280307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.243986 restraints weight = 4517.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.251646 restraints weight = 2516.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.256146 restraints weight = 1672.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.259197 restraints weight = 1260.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.260800 restraints weight = 1027.055| |-----------------------------------------------------------------------------| r_work (final): 0.4929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3327 Z= 0.143 Angle : 0.650 6.772 4495 Z= 0.329 Chirality : 0.045 0.188 462 Planarity : 0.005 0.057 573 Dihedral : 5.353 28.608 434 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.79 % Allowed : 15.48 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -2.05 (0.42), residues: 377 helix: -1.80 (0.38), residues: 162 sheet: -0.48 (0.93), residues: 30 loop : -0.95 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.012 0.001 TYR A 90 PHE 0.020 0.001 PHE A 368 TRP 0.043 0.002 TRP A 312 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3327) covalent geometry : angle 0.65037 ( 4495) hydrogen bonds : bond 0.04442 ( 101) hydrogen bonds : angle 6.24413 ( 285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.0716 time to fit residues: 6.1278 Evaluate side-chains 66 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 367 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 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 = 0.5087 r_free = 0.5087 target = 0.281072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.242650 restraints weight = 4187.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.250609 restraints weight = 2244.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.255553 restraints weight = 1452.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.258704 restraints weight = 1074.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.260467 restraints weight = 871.962| |-----------------------------------------------------------------------------| r_work (final): 0.4924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3327 Z= 0.156 Angle : 0.661 7.163 4495 Z= 0.331 Chirality : 0.046 0.200 462 Planarity : 0.005 0.054 573 Dihedral : 5.374 27.739 434 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.79 % Allowed : 16.07 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -2.09 (0.42), residues: 377 helix: -1.80 (0.38), residues: 162 sheet: -0.61 (0.88), residues: 35 loop : -0.98 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 369 TYR 0.011 0.001 TYR A 90 PHE 0.021 0.002 PHE A 368 TRP 0.015 0.002 TRP A 312 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3327) covalent geometry : angle 0.66126 ( 4495) hydrogen bonds : bond 0.04366 ( 101) hydrogen bonds : angle 6.31401 ( 285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ILE cc_start: 0.7366 (mt) cc_final: 0.7142 (tp) REVERT: A 312 TRP cc_start: 0.5129 (m100) cc_final: 0.4533 (m100) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.0809 time to fit residues: 6.7898 Evaluate side-chains 69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 368 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** 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 = 0.5077 r_free = 0.5077 target = 0.277952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.238558 restraints weight = 4546.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.246503 restraints weight = 2530.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.251097 restraints weight = 1696.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.253986 restraints weight = 1298.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.255540 restraints weight = 1088.157| |-----------------------------------------------------------------------------| r_work (final): 0.4884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3327 Z= 0.159 Angle : 0.686 8.969 4495 Z= 0.341 Chirality : 0.045 0.198 462 Planarity : 0.005 0.056 573 Dihedral : 5.354 29.177 434 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.79 % Allowed : 15.18 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -2.07 (0.42), residues: 377 helix: -1.80 (0.38), residues: 165 sheet: -0.92 (0.86), residues: 35 loop : -0.85 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 369 TYR 0.012 0.001 TYR A 90 PHE 0.020 0.002 PHE A 368 TRP 0.011 0.002 TRP A 358 HIS 0.004 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3327) covalent geometry : angle 0.68582 ( 4495) hydrogen bonds : bond 0.04203 ( 101) hydrogen bonds : angle 6.24326 ( 285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.5645 (m100) cc_final: 0.4402 (m100) outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.0804 time to fit residues: 6.7483 Evaluate side-chains 69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.278911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.239883 restraints weight = 4492.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.247586 restraints weight = 2445.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.252381 restraints weight = 1626.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.255405 restraints weight = 1236.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.256868 restraints weight = 1029.840| |-----------------------------------------------------------------------------| r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5366 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3327 Z= 0.146 Angle : 0.690 10.147 4495 Z= 0.339 Chirality : 0.045 0.210 462 Planarity : 0.005 0.054 573 Dihedral : 5.251 28.293 434 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.38 % Allowed : 15.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -2.05 (0.43), residues: 377 helix: -1.76 (0.39), residues: 161 sheet: -1.12 (0.84), residues: 35 loop : -0.84 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.012 0.001 TYR A 90 PHE 0.018 0.001 PHE A 368 TRP 0.013 0.002 TRP A 241 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3327) covalent geometry : angle 0.69042 ( 4495) hydrogen bonds : bond 0.04147 ( 101) hydrogen bonds : angle 6.11515 ( 285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.0645 time to fit residues: 5.2205 Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5069 r_free = 0.5069 target = 0.277432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.238535 restraints weight = 4197.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.245474 restraints weight = 2386.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.249809 restraints weight = 1624.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.252584 restraints weight = 1252.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.254229 restraints weight = 1049.780| |-----------------------------------------------------------------------------| r_work (final): 0.4869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3327 Z= 0.182 Angle : 0.758 9.487 4495 Z= 0.372 Chirality : 0.047 0.217 462 Planarity : 0.005 0.057 573 Dihedral : 5.543 29.210 434 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.68 % Allowed : 17.26 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -2.22 (0.43), residues: 377 helix: -1.89 (0.38), residues: 163 sheet: -1.85 (1.01), residues: 26 loop : -0.85 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 369 TYR 0.014 0.002 TYR A 378 PHE 0.018 0.002 PHE A 368 TRP 0.012 0.002 TRP A 249 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3327) covalent geometry : angle 0.75826 ( 4495) hydrogen bonds : bond 0.04571 ( 101) hydrogen bonds : angle 6.36422 ( 285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0709 time to fit residues: 5.6634 Evaluate side-chains 69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 216 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.0010 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.281017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.242806 restraints weight = 4469.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.250097 restraints weight = 2545.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.254800 restraints weight = 1716.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.257729 restraints weight = 1319.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.259147 restraints weight = 1100.577| |-----------------------------------------------------------------------------| r_work (final): 0.4926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3327 Z= 0.139 Angle : 0.711 10.050 4495 Z= 0.346 Chirality : 0.046 0.230 462 Planarity : 0.005 0.054 573 Dihedral : 5.280 28.745 434 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.79 % Allowed : 18.45 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -2.06 (0.43), residues: 377 helix: -1.75 (0.39), residues: 162 sheet: -1.97 (0.98), residues: 26 loop : -0.75 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.011 0.001 TYR A 90 PHE 0.017 0.001 PHE A 368 TRP 0.015 0.002 TRP A 285 HIS 0.005 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3327) covalent geometry : angle 0.71097 ( 4495) hydrogen bonds : bond 0.04125 ( 101) hydrogen bonds : angle 6.06093 ( 285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 754 Ramachandran restraints generated. 377 Oldfield, 0 Emsley, 377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.0741 time to fit residues: 5.6862 Evaluate side-chains 63 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 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 = 0.5169 r_free = 0.5169 target = 0.287135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.254807 restraints weight = 4680.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.261103 restraints weight = 2763.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.265084 restraints weight = 1904.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.267404 restraints weight = 1471.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.268660 restraints weight = 1239.633| |-----------------------------------------------------------------------------| r_work (final): 0.5016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3327 Z= 0.134 Angle : 0.709 10.173 4495 Z= 0.343 Chirality : 0.045 0.232 462 Planarity : 0.004 0.055 573 Dihedral : 5.176 28.002 434 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.19 % Allowed : 19.05 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.27 % 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 aren not related in a simple way. whole: -2.02 (0.44), residues: 377 helix: -1.75 (0.38), residues: 163 sheet: -1.41 (0.80), residues: 37 loop : -0.72 (0.51), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 218 TYR 0.010 0.001 TYR A 90 PHE 0.017 0.001 PHE A 368 TRP 0.014 0.002 TRP A 285 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3327) covalent geometry : angle 0.70875 ( 4495) hydrogen bonds : bond 0.03984 ( 101) hydrogen bonds : angle 5.89775 ( 285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 905.23 seconds wall clock time: 16 minutes 14.08 seconds (974.08 seconds total)