Starting phenix.real_space_refine on Tue Mar 3 14:29:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq3_32084/03_2026/7vq3_32084.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq3_32084/03_2026/7vq3_32084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vq3_32084/03_2026/7vq3_32084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq3_32084/03_2026/7vq3_32084.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq3_32084/03_2026/7vq3_32084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq3_32084/03_2026/7vq3_32084.cif" } resolution = 3.2 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= 0.005 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 34 5.16 5 C 4070 2.51 5 N 1052 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6306 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 1.69, per 1000 atoms: 0.27 Number of scatterers: 6306 At special positions: 0 Unit cell: (84.162, 84.162, 109.512, 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 34 16.00 O 1150 8.00 N 1052 7.00 C 4070 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: 0.37 Conformation dependent library (CDL) restraints added in 332.0 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.4% alpha, 0.0% 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 1 through 18 removed outlier: 3.531A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.709A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.854A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 134 through 151 Processing helix chain 'A' and resid 158 through 183 removed outlier: 3.673A pdb=" N GLU A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.395A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.543A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 removed outlier: 3.640A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.030A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.658A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 4.206A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.531A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.709A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.854A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 158 through 183 removed outlier: 3.673A pdb=" N GLU B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.395A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.543A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 294 removed outlier: 3.640A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 4.030A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.658A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 4.206A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 515 hydrogen bonds defined for protein. 1545 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: 0.98 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2010 1.34 - 1.46: 1360 1.46 - 1.58: 3004 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CB THR B 168 " pdb=" CG2 THR B 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CB MET A 377 " pdb=" CG MET A 377 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CB MET B 377 " pdb=" CG MET B 377 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CB THR B 73 " pdb=" CG2 THR B 73 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.82e-01 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 8260 1.13 - 2.27: 370 2.27 - 3.40: 44 3.40 - 4.54: 10 4.54 - 5.67: 8 Bond angle restraints: 8692 Sorted by residual: angle pdb=" C VAL A 105 " pdb=" N GLU A 106 " pdb=" CA GLU A 106 " ideal model delta sigma weight residual 119.78 122.06 -2.28 1.24e+00 6.50e-01 3.37e+00 angle pdb=" C VAL B 105 " pdb=" N GLU B 106 " pdb=" CA GLU B 106 " ideal model delta sigma weight residual 119.78 122.06 -2.28 1.24e+00 6.50e-01 3.37e+00 angle pdb=" N GLU A 307 " pdb=" CA GLU A 307 " pdb=" C GLU A 307 " ideal model delta sigma weight residual 111.11 113.15 -2.04 1.20e+00 6.94e-01 2.88e+00 angle pdb=" N GLU B 307 " pdb=" CA GLU B 307 " pdb=" C GLU B 307 " ideal model delta sigma weight residual 111.11 113.15 -2.04 1.20e+00 6.94e-01 2.88e+00 angle pdb=" C PHE B 182 " pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 121.97 119.01 2.96 1.80e+00 3.09e-01 2.70e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 3366 16.81 - 33.61: 404 33.61 - 50.42: 74 50.42 - 67.23: 2 67.23 - 84.03: 10 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: dihedral pdb=" CA HIS B 259 " pdb=" C HIS B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA HIS A 259 " pdb=" C HIS A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB GLU B 307 " pdb=" CG GLU B 307 " pdb=" CD GLU B 307 " pdb=" OE1 GLU B 307 " ideal model delta sinusoidal sigma weight residual 0.00 84.03 -84.03 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 516 0.027 - 0.054: 346 0.054 - 0.081: 98 0.081 - 0.108: 20 0.108 - 0.135: 16 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA THR A 308 " pdb=" N THR A 308 " pdb=" C THR A 308 " pdb=" CB THR A 308 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA THR B 308 " pdb=" N THR B 308 " pdb=" C THR B 308 " pdb=" CB THR B 308 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 298 " pdb=" N ILE A 298 " pdb=" C ILE A 298 " pdb=" CB ILE A 298 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 365 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 365 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 257 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 258 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.019 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 42 2.63 - 3.20: 5928 3.20 - 3.76: 9359 3.76 - 4.33: 12910 4.33 - 4.90: 21301 Nonbonded interactions: 49540 Sorted by model distance: nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.061 3.040 nonbonded pdb=" OG SER A 376 " pdb=" OH TYR B 291 " model vdw 2.061 3.040 nonbonded pdb=" OE1 GLU B 213 " pdb=" ND2 ASN B 232 " model vdw 2.284 3.120 nonbonded pdb=" OE1 GLU A 213 " pdb=" ND2 ASN A 232 " model vdw 2.284 3.120 nonbonded pdb=" O SER A 294 " pdb=" NE2 GLN A 297 " model vdw 2.316 3.120 ... (remaining 49535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.005 0.053 6434 Z= 0.219 Angle : 0.550 5.673 8692 Z= 0.316 Chirality : 0.039 0.135 996 Planarity : 0.004 0.037 1090 Dihedral : 14.665 84.030 2352 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: -0.93 (0.28), residues: 792 helix: 0.06 (0.18), residues: 642 sheet: None (None), residues: 0 loop : -3.31 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 9 TYR 0.012 0.001 TYR B 291 PHE 0.012 0.001 PHE A 200 TRP 0.014 0.002 TRP B 129 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 6434) covalent geometry : angle 0.54998 ( 8692) hydrogen bonds : bond 0.11844 ( 515) hydrogen bonds : angle 5.39677 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.233 Fit side-chains REVERT: A 50 TYR cc_start: 0.7738 (t80) cc_final: 0.7338 (t80) REVERT: A 229 ARG cc_start: 0.6960 (mmt90) cc_final: 0.6567 (ttp80) REVERT: A 261 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7021 (tt0) REVERT: A 387 LYS cc_start: 0.7991 (mttt) cc_final: 0.7667 (mptt) REVERT: B 229 ARG cc_start: 0.6964 (mmt90) cc_final: 0.6577 (ttp80) REVERT: B 261 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7002 (tt0) REVERT: B 387 LYS cc_start: 0.8007 (mttt) cc_final: 0.7690 (mptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0958 time to fit residues: 15.2969 Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 96 GLN A 251 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 361 ASN B 54 ASN B 96 GLN B 251 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 361 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118352 restraints weight = 7489.834| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.03 r_work: 0.3228 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6434 Z= 0.149 Angle : 0.522 5.900 8692 Z= 0.277 Chirality : 0.038 0.129 996 Planarity : 0.004 0.044 1090 Dihedral : 4.062 19.247 858 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.58 % Allowed : 9.34 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.31), residues: 792 helix: 1.66 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.63 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.014 0.001 TYR B 236 PHE 0.013 0.001 PHE A 206 TRP 0.008 0.001 TRP B 129 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6434) covalent geometry : angle 0.52168 ( 8692) hydrogen bonds : bond 0.05299 ( 515) hydrogen bonds : angle 4.12307 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.162 Fit side-chains REVERT: A 67 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8402 (mm-30) REVERT: A 229 ARG cc_start: 0.6996 (mmt90) cc_final: 0.6378 (ttp80) REVERT: A 261 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7244 (tt0) REVERT: A 291 TYR cc_start: 0.7496 (m-80) cc_final: 0.7197 (m-10) REVERT: A 297 GLN cc_start: 0.7946 (mm110) cc_final: 0.7632 (mm110) REVERT: A 387 LYS cc_start: 0.7946 (mttt) cc_final: 0.7551 (mptt) REVERT: B 67 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 229 ARG cc_start: 0.7010 (mmt90) cc_final: 0.6317 (ttp80) REVERT: B 261 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7250 (tt0) REVERT: B 291 TYR cc_start: 0.7482 (m-80) cc_final: 0.7190 (m-10) REVERT: B 297 GLN cc_start: 0.7948 (mm110) cc_final: 0.7630 (mm110) REVERT: B 387 LYS cc_start: 0.7969 (mttt) cc_final: 0.7572 (mptt) outliers start: 11 outliers final: 7 residues processed: 112 average time/residue: 0.0889 time to fit residues: 12.8375 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 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 = 0.3834 r_free = 0.3834 target = 0.161021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119916 restraints weight = 7566.754| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.12 r_work: 0.3172 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6434 Z= 0.158 Angle : 0.510 5.788 8692 Z= 0.273 Chirality : 0.038 0.131 996 Planarity : 0.004 0.045 1090 Dihedral : 3.979 19.487 858 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.01 % Allowed : 12.64 % Favored : 85.34 % 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: 1.95 (0.31), residues: 792 helix: 2.10 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.90 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.011 0.001 TYR B 39 PHE 0.015 0.001 PHE B 206 TRP 0.009 0.001 TRP B 129 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6434) covalent geometry : angle 0.51003 ( 8692) hydrogen bonds : bond 0.05300 ( 515) hydrogen bonds : angle 4.00026 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.237 Fit side-chains REVERT: A 387 LYS cc_start: 0.8015 (mttt) cc_final: 0.7587 (mptt) REVERT: B 230 LYS cc_start: 0.8443 (tptt) cc_final: 0.7935 (ttmt) REVERT: B 387 LYS cc_start: 0.8025 (mttt) cc_final: 0.7601 (mptt) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.0727 time to fit residues: 9.7656 Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.164376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121932 restraints weight = 7551.664| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.18 r_work: 0.3251 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6434 Z= 0.119 Angle : 0.468 6.300 8692 Z= 0.249 Chirality : 0.037 0.129 996 Planarity : 0.004 0.045 1090 Dihedral : 3.799 17.203 858 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.58 % Allowed : 14.80 % Favored : 83.62 % 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: 2.59 (0.31), residues: 792 helix: 2.55 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.74 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.009 0.001 TYR B 39 PHE 0.013 0.001 PHE A 206 TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6434) covalent geometry : angle 0.46821 ( 8692) hydrogen bonds : bond 0.04389 ( 515) hydrogen bonds : angle 3.78980 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.175 Fit side-chains REVERT: A 230 LYS cc_start: 0.8344 (tptt) cc_final: 0.7899 (tptt) REVERT: A 261 GLN cc_start: 0.8307 (tp-100) cc_final: 0.7408 (tt0) REVERT: A 387 LYS cc_start: 0.7838 (mttt) cc_final: 0.7447 (mptt) REVERT: B 229 ARG cc_start: 0.7013 (mmt90) cc_final: 0.6711 (mmt180) REVERT: B 230 LYS cc_start: 0.8404 (tptt) cc_final: 0.7965 (ttmt) REVERT: B 261 GLN cc_start: 0.8303 (tp-100) cc_final: 0.7391 (tt0) REVERT: B 387 LYS cc_start: 0.7845 (mttt) cc_final: 0.7452 (mptt) outliers start: 11 outliers final: 9 residues processed: 101 average time/residue: 0.0826 time to fit residues: 10.8844 Evaluate side-chains 91 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 285 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 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 = 0.3865 r_free = 0.3865 target = 0.163242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122366 restraints weight = 7519.290| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.04 r_work: 0.3282 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6434 Z= 0.119 Angle : 0.486 7.452 8692 Z= 0.252 Chirality : 0.037 0.135 996 Planarity : 0.004 0.045 1090 Dihedral : 3.735 16.551 858 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.44 % Allowed : 16.24 % Favored : 81.32 % 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: 2.86 (0.31), residues: 792 helix: 2.74 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.64 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.009 0.001 TYR B 39 PHE 0.013 0.001 PHE B 206 TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6434) covalent geometry : angle 0.48562 ( 8692) hydrogen bonds : bond 0.04321 ( 515) hydrogen bonds : angle 3.75456 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.258 Fit side-chains REVERT: A 230 LYS cc_start: 0.8432 (tptt) cc_final: 0.7997 (tptt) REVERT: A 261 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7477 (tt0) REVERT: A 387 LYS cc_start: 0.7980 (mttt) cc_final: 0.7579 (mptt) REVERT: B 230 LYS cc_start: 0.8457 (tptt) cc_final: 0.8031 (ttmt) REVERT: B 261 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7465 (tt0) REVERT: B 387 LYS cc_start: 0.8003 (mttt) cc_final: 0.7615 (mptt) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.0846 time to fit residues: 10.5469 Evaluate side-chains 86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118305 restraints weight = 7467.613| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.04 r_work: 0.3239 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6434 Z= 0.140 Angle : 0.492 6.889 8692 Z= 0.258 Chirality : 0.037 0.127 996 Planarity : 0.004 0.045 1090 Dihedral : 3.798 16.786 858 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.44 % Allowed : 15.66 % Favored : 81.90 % 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: 2.87 (0.31), residues: 792 helix: 2.74 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.62 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.009 0.001 TYR B 39 PHE 0.014 0.001 PHE B 206 TRP 0.007 0.001 TRP A 129 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6434) covalent geometry : angle 0.49231 ( 8692) hydrogen bonds : bond 0.04787 ( 515) hydrogen bonds : angle 3.80173 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.232 Fit side-chains REVERT: A 230 LYS cc_start: 0.8470 (tptt) cc_final: 0.8044 (tptt) REVERT: A 261 GLN cc_start: 0.8366 (tp-100) cc_final: 0.7500 (tt0) REVERT: A 297 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7873 (mm110) REVERT: A 322 LYS cc_start: 0.8218 (tttm) cc_final: 0.7865 (tppt) REVERT: A 387 LYS cc_start: 0.7968 (mttt) cc_final: 0.7547 (mptt) REVERT: B 230 LYS cc_start: 0.8427 (tptt) cc_final: 0.8016 (ttmt) REVERT: B 261 GLN cc_start: 0.8369 (tp-100) cc_final: 0.7478 (tt0) REVERT: B 297 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7879 (mm110) REVERT: B 322 LYS cc_start: 0.8222 (tttm) cc_final: 0.7861 (tppt) REVERT: B 387 LYS cc_start: 0.7987 (mttt) cc_final: 0.7575 (mptt) outliers start: 17 outliers final: 11 residues processed: 100 average time/residue: 0.0776 time to fit residues: 10.5115 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122460 restraints weight = 7506.935| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.04 r_work: 0.3272 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6434 Z= 0.120 Angle : 0.480 7.057 8692 Z= 0.250 Chirality : 0.037 0.129 996 Planarity : 0.004 0.045 1090 Dihedral : 3.733 16.717 858 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.30 % Allowed : 16.67 % Favored : 81.03 % 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: 3.06 (0.31), residues: 792 helix: 2.88 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.58 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 265 TYR 0.008 0.001 TYR B 39 PHE 0.013 0.001 PHE B 206 TRP 0.008 0.001 TRP B 57 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6434) covalent geometry : angle 0.47956 ( 8692) hydrogen bonds : bond 0.04309 ( 515) hydrogen bonds : angle 3.71807 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.229 Fit side-chains REVERT: A 230 LYS cc_start: 0.8499 (tptt) cc_final: 0.8124 (tptt) REVERT: A 261 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7579 (tt0) REVERT: A 322 LYS cc_start: 0.8169 (tttm) cc_final: 0.7842 (tppt) REVERT: A 387 LYS cc_start: 0.7981 (mttt) cc_final: 0.7548 (mptt) REVERT: B 230 LYS cc_start: 0.8358 (tptt) cc_final: 0.7976 (ttmt) REVERT: B 261 GLN cc_start: 0.8363 (tp-100) cc_final: 0.7563 (tt0) REVERT: B 322 LYS cc_start: 0.8216 (tttm) cc_final: 0.7893 (tppt) REVERT: B 387 LYS cc_start: 0.7999 (mttt) cc_final: 0.7570 (mptt) outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.0768 time to fit residues: 10.5178 Evaluate side-chains 101 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 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 297 GLN B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.162254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121239 restraints weight = 7543.102| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.04 r_work: 0.3233 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6434 Z= 0.134 Angle : 0.515 7.059 8692 Z= 0.269 Chirality : 0.037 0.132 996 Planarity : 0.004 0.047 1090 Dihedral : 3.766 16.040 858 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.02 % Allowed : 16.67 % Favored : 80.32 % 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: 2.99 (0.31), residues: 792 helix: 2.82 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.54 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.014 0.001 TYR A 50 PHE 0.014 0.001 PHE B 206 TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6434) covalent geometry : angle 0.51537 ( 8692) hydrogen bonds : bond 0.04540 ( 515) hydrogen bonds : angle 3.79408 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.240 Fit side-chains REVERT: A 213 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7827 (tt0) REVERT: A 230 LYS cc_start: 0.8477 (tptt) cc_final: 0.8099 (tptt) REVERT: A 261 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7556 (tt0) REVERT: A 297 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7621 (mm110) REVERT: A 322 LYS cc_start: 0.8200 (tttm) cc_final: 0.7882 (tppt) REVERT: A 387 LYS cc_start: 0.7992 (mttt) cc_final: 0.7556 (mptt) REVERT: B 213 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7805 (tt0) REVERT: B 230 LYS cc_start: 0.8348 (tptt) cc_final: 0.7998 (ttmt) REVERT: B 261 GLN cc_start: 0.8383 (tp-100) cc_final: 0.7555 (tt0) REVERT: B 297 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7618 (mm110) REVERT: B 322 LYS cc_start: 0.8245 (tttm) cc_final: 0.7928 (tppt) REVERT: B 387 LYS cc_start: 0.8026 (mttt) cc_final: 0.7585 (mptt) outliers start: 21 outliers final: 17 residues processed: 107 average time/residue: 0.0813 time to fit residues: 11.5482 Evaluate side-chains 108 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 0.0030 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.163723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122812 restraints weight = 7548.225| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.04 r_work: 0.3282 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6434 Z= 0.121 Angle : 0.502 7.200 8692 Z= 0.262 Chirality : 0.037 0.130 996 Planarity : 0.004 0.047 1090 Dihedral : 3.734 16.139 858 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.44 % Allowed : 17.82 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.10 (0.31), residues: 792 helix: 2.90 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.54 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.007 0.001 TYR B 39 PHE 0.013 0.001 PHE A 206 TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6434) covalent geometry : angle 0.50183 ( 8692) hydrogen bonds : bond 0.04213 ( 515) hydrogen bonds : angle 3.72624 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.291 Fit side-chains REVERT: A 230 LYS cc_start: 0.8457 (tptt) cc_final: 0.8037 (tttm) REVERT: A 261 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7575 (tt0) REVERT: A 322 LYS cc_start: 0.8190 (tttm) cc_final: 0.7869 (tppt) REVERT: A 324 MET cc_start: 0.7896 (ttm) cc_final: 0.7587 (ttm) REVERT: A 387 LYS cc_start: 0.7982 (mttt) cc_final: 0.7556 (mptt) REVERT: B 50 TYR cc_start: 0.8022 (t80) cc_final: 0.7788 (t80) REVERT: B 230 LYS cc_start: 0.8306 (tptt) cc_final: 0.8010 (ttmt) REVERT: B 261 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7557 (tt0) REVERT: B 322 LYS cc_start: 0.8206 (tttm) cc_final: 0.7873 (tppt) REVERT: B 324 MET cc_start: 0.7887 (ttm) cc_final: 0.7578 (ttm) REVERT: B 387 LYS cc_start: 0.8017 (mttt) cc_final: 0.7593 (mptt) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.0799 time to fit residues: 11.4280 Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.163887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122721 restraints weight = 7439.573| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.04 r_work: 0.3261 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6434 Z= 0.120 Angle : 0.509 7.282 8692 Z= 0.266 Chirality : 0.037 0.130 996 Planarity : 0.004 0.047 1090 Dihedral : 3.708 15.201 858 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.59 % Allowed : 17.96 % Favored : 79.45 % 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: 3.14 (0.31), residues: 792 helix: 2.92 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.50 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.024 0.001 TYR B 236 PHE 0.030 0.001 PHE B 206 TRP 0.007 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6434) covalent geometry : angle 0.50924 ( 8692) hydrogen bonds : bond 0.04197 ( 515) hydrogen bonds : angle 3.70710 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.190 Fit side-chains REVERT: A 213 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7681 (tt0) REVERT: A 230 LYS cc_start: 0.8417 (tptt) cc_final: 0.7987 (tttm) REVERT: A 261 GLN cc_start: 0.8293 (tp-100) cc_final: 0.7547 (tt0) REVERT: A 322 LYS cc_start: 0.8174 (tttm) cc_final: 0.7840 (tppt) REVERT: A 324 MET cc_start: 0.7899 (ttm) cc_final: 0.7583 (ttm) REVERT: A 387 LYS cc_start: 0.7979 (mttt) cc_final: 0.7522 (mptt) REVERT: A 394 GLU cc_start: 0.7864 (tp30) cc_final: 0.7385 (pt0) REVERT: B 41 TYR cc_start: 0.6755 (m-80) cc_final: 0.5751 (m-80) REVERT: B 50 TYR cc_start: 0.8059 (t80) cc_final: 0.7809 (t80) REVERT: B 213 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7667 (tt0) REVERT: B 230 LYS cc_start: 0.8240 (tptt) cc_final: 0.7969 (ttmt) REVERT: B 261 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7547 (tt0) REVERT: B 322 LYS cc_start: 0.8181 (tttm) cc_final: 0.7837 (tppt) REVERT: B 324 MET cc_start: 0.7896 (ttm) cc_final: 0.7582 (ttm) REVERT: B 387 LYS cc_start: 0.7995 (mttt) cc_final: 0.7549 (mptt) outliers start: 18 outliers final: 16 residues processed: 104 average time/residue: 0.0934 time to fit residues: 12.7272 Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.165075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124159 restraints weight = 7483.643| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.04 r_work: 0.3301 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6434 Z= 0.117 Angle : 0.499 7.121 8692 Z= 0.261 Chirality : 0.037 0.153 996 Planarity : 0.004 0.048 1090 Dihedral : 3.692 16.451 858 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.73 % Allowed : 18.10 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.19 (0.31), residues: 792 helix: 2.96 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.47 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 312 TYR 0.025 0.001 TYR B 236 PHE 0.029 0.001 PHE A 206 TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6434) covalent geometry : angle 0.49853 ( 8692) hydrogen bonds : bond 0.04117 ( 515) hydrogen bonds : angle 3.67773 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1592.26 seconds wall clock time: 27 minutes 56.57 seconds (1676.57 seconds total)