Starting phenix.real_space_refine on Fri Aug 22 16:21:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdo_17616/08_2025/8pdo_17616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdo_17616/08_2025/8pdo_17616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2025/8pdo_17616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2025/8pdo_17616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2025/8pdo_17616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2025/8pdo_17616.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 22 5.16 5 C 3564 2.51 5 N 990 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 5722 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Time building chain proxies: 1.78, per 1000 atoms: 0.31 Number of scatterers: 5722 At special positions: 0 Unit cell: (114.45, 79.8, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 14 15.00 O 1132 8.00 N 990 7.00 C 3564 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: 0.56 Conformation dependent library (CDL) restraints added in 232.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 69.1% alpha, 2.6% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.595A pdb=" N TYR A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.620A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 120 through 141 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.584A pdb=" N GLN B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 151 " --> pdb=" O GLN B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 156 through 171 removed outlier: 3.854A pdb=" N LYS B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.846A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.789A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 256 through 268 removed outlier: 3.613A pdb=" N ARG B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 296 removed outlier: 4.860A pdb=" N LYS B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.890A pdb=" N GLY B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 344 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 35 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 336 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.73 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: 1845 1.34 - 1.46: 846 1.46 - 1.57: 3079 1.57 - 1.69: 27 1.69 - 1.81: 38 Bond restraints: 5835 Sorted by residual: bond pdb=" C VAL A 35 " pdb=" N THR A 36 " ideal model delta sigma weight residual 1.331 1.303 0.027 1.24e-02 6.50e+03 4.88e+00 bond pdb=" CB VAL B 92 " pdb=" CG1 VAL B 92 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CA GLU B 20 " pdb=" C GLU B 20 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.66e-02 3.63e+03 3.98e+00 bond pdb=" CB VAL A 92 " pdb=" CG1 VAL A 92 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.63e+00 bond pdb=" N LYS B 239 " pdb=" CA LYS B 239 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.33e-02 5.65e+03 2.83e+00 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 7551 1.43 - 2.86: 349 2.86 - 4.29: 31 4.29 - 5.72: 3 5.72 - 7.15: 4 Bond angle restraints: 7938 Sorted by residual: angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.60 115.45 7.15 1.56e+00 4.11e-01 2.10e+01 angle pdb=" N ILE A 6 " pdb=" CA ILE A 6 " pdb=" C ILE A 6 " ideal model delta sigma weight residual 106.21 108.97 -2.76 1.07e+00 8.73e-01 6.66e+00 angle pdb=" C GLN A 91 " pdb=" N VAL A 92 " pdb=" CA VAL A 92 " ideal model delta sigma weight residual 120.63 123.86 -3.23 1.33e+00 5.65e-01 5.91e+00 angle pdb=" N LYS B 239 " pdb=" CA LYS B 239 " pdb=" C LYS B 239 " ideal model delta sigma weight residual 112.54 109.71 2.83 1.22e+00 6.72e-01 5.38e+00 angle pdb=" CA GLU B 20 " pdb=" C GLU B 20 " pdb=" N SER B 21 " ideal model delta sigma weight residual 117.96 120.71 -2.75 1.23e+00 6.61e-01 4.98e+00 ... (remaining 7933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3187 17.53 - 35.05: 315 35.05 - 52.58: 59 52.58 - 70.11: 13 70.11 - 87.64: 21 Dihedral angle restraints: 3595 sinusoidal: 1563 harmonic: 2032 Sorted by residual: dihedral pdb=" CA GLY B 311 " pdb=" C GLY B 311 " pdb=" N LEU B 312 " pdb=" CA LEU B 312 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LEU B 52 " pdb=" C LEU B 52 " pdb=" N TYR B 53 " pdb=" CA TYR B 53 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ALA B 251 " pdb=" C ALA B 251 " pdb=" N TYR B 252 " pdb=" CA TYR B 252 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 652 0.042 - 0.083: 226 0.083 - 0.125: 48 0.125 - 0.166: 8 0.166 - 0.208: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CB VAL B 35 " pdb=" CA VAL B 35 " pdb=" CG1 VAL B 35 " pdb=" CG2 VAL B 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE A 25 " pdb=" N ILE A 25 " pdb=" C ILE A 25 " pdb=" CB ILE A 25 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 933 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 198 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 199 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 53 " 0.007 2.00e-02 2.50e+03 1.34e-02 3.60e+00 pdb=" CG TYR A 53 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 53 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 53 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 53 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 53 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 53 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 73 " 0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C C 73 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C C 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C C 73 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 73 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C C 73 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C C 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 73 " -0.005 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 51 2.63 - 3.20: 5295 3.20 - 3.77: 9054 3.77 - 4.33: 12859 4.33 - 4.90: 20585 Nonbonded interactions: 47844 Sorted by model distance: nonbonded pdb=" O LEU A 18 " pdb=" OG SER B 233 " model vdw 2.068 3.040 nonbonded pdb=" OG SER A 277 " pdb=" OD1 ASN A 320 " model vdw 2.138 3.040 nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 95 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 338 " pdb=" OP2 C C 74 " model vdw 2.232 3.040 nonbonded pdb=" NH1 ARG A 27 " pdb=" O THR B 236 " model vdw 2.241 3.120 ... (remaining 47839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.950 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 5835 Z= 0.278 Angle : 0.664 7.149 7938 Z= 0.393 Chirality : 0.044 0.208 936 Planarity : 0.004 0.051 962 Dihedral : 15.615 87.636 2291 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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 aren not related in a simple way. whole: 0.19 (0.32), residues: 694 helix: 0.59 (0.24), residues: 470 sheet: -1.01 (0.87), residues: 30 loop : -0.60 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.031 0.003 TYR A 53 PHE 0.017 0.002 PHE B 224 TRP 0.006 0.001 TRP B 123 HIS 0.004 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 5835) covalent geometry : angle 0.66374 ( 7938) hydrogen bonds : bond 0.12984 ( 336) hydrogen bonds : angle 5.84367 ( 987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.215 Fit side-chains REVERT: A 78 ARG cc_start: 0.7403 (mmm160) cc_final: 0.5880 (tpt-90) REVERT: A 249 MET cc_start: 0.7654 (mmt) cc_final: 0.7430 (mmt) REVERT: A 266 ARG cc_start: 0.7783 (tmt170) cc_final: 0.5836 (tpt170) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1221 time to fit residues: 12.6420 Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.0060 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138628 restraints weight = 6731.366| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.52 r_work: 0.3442 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5835 Z= 0.137 Angle : 0.481 6.143 7938 Z= 0.260 Chirality : 0.039 0.143 936 Planarity : 0.004 0.046 962 Dihedral : 11.435 73.999 987 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.50 % Allowed : 5.20 % Favored : 94.30 % 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 aren not related in a simple way. whole: 0.84 (0.32), residues: 694 helix: 1.17 (0.24), residues: 474 sheet: -0.94 (0.88), residues: 30 loop : -0.61 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 208 TYR 0.017 0.002 TYR A 53 PHE 0.013 0.001 PHE B 224 TRP 0.005 0.001 TRP B 123 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5835) covalent geometry : angle 0.48056 ( 7938) hydrogen bonds : bond 0.04643 ( 336) hydrogen bonds : angle 4.42160 ( 987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.233 Fit side-chains REVERT: A 78 ARG cc_start: 0.7497 (mmm160) cc_final: 0.5537 (tpt-90) REVERT: A 266 ARG cc_start: 0.7860 (tmt170) cc_final: 0.5727 (tpt170) REVERT: A 337 MET cc_start: 0.8716 (tpp) cc_final: 0.8480 (mmp) REVERT: B 196 LYS cc_start: 0.7831 (mttt) cc_final: 0.7598 (ttpp) outliers start: 3 outliers final: 1 residues processed: 81 average time/residue: 0.1195 time to fit residues: 11.7344 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.154023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132606 restraints weight = 6620.842| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.61 r_work: 0.3385 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5835 Z= 0.173 Angle : 0.496 6.190 7938 Z= 0.267 Chirality : 0.040 0.139 936 Planarity : 0.004 0.043 962 Dihedral : 11.438 74.161 987 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.34 % Allowed : 8.56 % Favored : 91.11 % 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 aren not related in a simple way. whole: 0.89 (0.33), residues: 694 helix: 1.18 (0.24), residues: 474 sheet: -1.07 (0.89), residues: 30 loop : -0.46 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 208 TYR 0.015 0.002 TYR A 59 PHE 0.013 0.002 PHE B 224 TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5835) covalent geometry : angle 0.49619 ( 7938) hydrogen bonds : bond 0.04716 ( 336) hydrogen bonds : angle 4.33470 ( 987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.164 Fit side-chains REVERT: A 78 ARG cc_start: 0.7430 (mmm160) cc_final: 0.5379 (tpt-90) REVERT: A 266 ARG cc_start: 0.7816 (tmt170) cc_final: 0.5581 (tpt170) REVERT: B 196 LYS cc_start: 0.7723 (mttt) cc_final: 0.7489 (ttpp) outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.1177 time to fit residues: 10.2622 Evaluate side-chains 70 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 188 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 63 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134776 restraints weight = 6717.433| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.57 r_work: 0.3455 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5835 Z= 0.129 Angle : 0.453 6.104 7938 Z= 0.244 Chirality : 0.039 0.168 936 Planarity : 0.004 0.041 962 Dihedral : 11.430 73.921 987 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.17 % Allowed : 8.72 % Favored : 90.10 % 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 aren not related in a simple way. whole: 1.06 (0.33), residues: 694 helix: 1.31 (0.24), residues: 480 sheet: -0.99 (0.89), residues: 30 loop : -0.47 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 208 TYR 0.011 0.001 TYR A 338 PHE 0.011 0.001 PHE B 224 TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5835) covalent geometry : angle 0.45303 ( 7938) hydrogen bonds : bond 0.04161 ( 336) hydrogen bonds : angle 4.14423 ( 987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.259 Fit side-chains REVERT: A 78 ARG cc_start: 0.7412 (mmm160) cc_final: 0.5387 (tpt-90) REVERT: A 266 ARG cc_start: 0.7735 (tmt170) cc_final: 0.4765 (mtt180) REVERT: B 117 HIS cc_start: 0.7250 (t70) cc_final: 0.6681 (t70) REVERT: B 139 LEU cc_start: 0.8260 (tp) cc_final: 0.7862 (tt) REVERT: B 196 LYS cc_start: 0.7689 (mttt) cc_final: 0.7418 (ttpp) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 0.1287 time to fit residues: 12.0152 Evaluate side-chains 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130172 restraints weight = 6820.293| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.67 r_work: 0.3374 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5835 Z= 0.188 Angle : 0.502 6.152 7938 Z= 0.268 Chirality : 0.041 0.171 936 Planarity : 0.004 0.039 962 Dihedral : 11.435 74.221 987 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.01 % Allowed : 10.74 % Favored : 88.26 % 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 aren not related in a simple way. whole: 0.86 (0.33), residues: 694 helix: 1.15 (0.24), residues: 480 sheet: -1.05 (0.89), residues: 30 loop : -0.49 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 208 TYR 0.016 0.002 TYR A 59 PHE 0.013 0.002 PHE B 224 TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5835) covalent geometry : angle 0.50166 ( 7938) hydrogen bonds : bond 0.04680 ( 336) hydrogen bonds : angle 4.25407 ( 987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.255 Fit side-chains REVERT: A 78 ARG cc_start: 0.7417 (mmm160) cc_final: 0.5350 (tpt-90) REVERT: A 135 MET cc_start: 0.6951 (ttt) cc_final: 0.6716 (ttt) REVERT: A 266 ARG cc_start: 0.7776 (tmt170) cc_final: 0.5524 (tpt170) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.1323 time to fit residues: 12.0779 Evaluate side-chains 74 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 41 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.170097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150928 restraints weight = 6545.916| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.42 r_work: 0.3562 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5835 Z= 0.110 Angle : 0.435 6.042 7938 Z= 0.234 Chirality : 0.038 0.138 936 Planarity : 0.004 0.041 962 Dihedral : 11.474 73.876 987 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.84 % Allowed : 11.58 % Favored : 87.58 % 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 aren not related in a simple way. whole: 1.33 (0.33), residues: 694 helix: 1.51 (0.25), residues: 476 sheet: -0.99 (0.88), residues: 30 loop : -0.30 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 208 TYR 0.012 0.001 TYR A 338 PHE 0.010 0.001 PHE B 224 TRP 0.005 0.001 TRP B 123 HIS 0.003 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5835) covalent geometry : angle 0.43497 ( 7938) hydrogen bonds : bond 0.03886 ( 336) hydrogen bonds : angle 4.01619 ( 987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.211 Fit side-chains REVERT: A 78 ARG cc_start: 0.7584 (mmm160) cc_final: 0.5700 (tpt-90) REVERT: A 135 MET cc_start: 0.7112 (ttt) cc_final: 0.6911 (ttt) REVERT: A 266 ARG cc_start: 0.7779 (tmt170) cc_final: 0.4931 (mtt180) REVERT: A 284 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 117 HIS cc_start: 0.7303 (t70) cc_final: 0.6729 (t70) REVERT: B 139 LEU cc_start: 0.8316 (tp) cc_final: 0.7920 (tt) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 0.1227 time to fit residues: 11.4825 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134851 restraints weight = 6715.988| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.65 r_work: 0.3389 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5835 Z= 0.173 Angle : 0.484 6.073 7938 Z= 0.259 Chirality : 0.040 0.156 936 Planarity : 0.004 0.041 962 Dihedral : 11.461 74.179 987 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.84 % Allowed : 13.26 % Favored : 85.91 % 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 aren not related in a simple way. whole: 0.99 (0.33), residues: 694 helix: 1.28 (0.24), residues: 480 sheet: -1.08 (0.87), residues: 30 loop : -0.54 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 208 TYR 0.015 0.002 TYR A 59 PHE 0.012 0.002 PHE B 224 TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5835) covalent geometry : angle 0.48354 ( 7938) hydrogen bonds : bond 0.04510 ( 336) hydrogen bonds : angle 4.15187 ( 987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.274 Fit side-chains REVERT: A 78 ARG cc_start: 0.7425 (mmm160) cc_final: 0.5379 (tpt-90) REVERT: A 135 MET cc_start: 0.7023 (ttt) cc_final: 0.6770 (ttt) REVERT: A 266 ARG cc_start: 0.7770 (tmt170) cc_final: 0.4629 (mtt180) REVERT: A 284 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 282 LEU cc_start: 0.8689 (mt) cc_final: 0.8429 (mt) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.1245 time to fit residues: 10.8232 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144633 restraints weight = 6537.972| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.40 r_work: 0.3470 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5835 Z= 0.135 Angle : 0.454 6.046 7938 Z= 0.244 Chirality : 0.039 0.138 936 Planarity : 0.004 0.040 962 Dihedral : 11.474 74.027 987 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.84 % Allowed : 13.09 % Favored : 86.07 % 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 aren not related in a simple way. whole: 1.12 (0.33), residues: 694 helix: 1.40 (0.24), residues: 480 sheet: -1.02 (0.88), residues: 30 loop : -0.57 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 208 TYR 0.011 0.001 TYR A 338 PHE 0.011 0.001 PHE B 224 TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5835) covalent geometry : angle 0.45361 ( 7938) hydrogen bonds : bond 0.04198 ( 336) hydrogen bonds : angle 4.06011 ( 987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.219 Fit side-chains REVERT: A 78 ARG cc_start: 0.7501 (mmm160) cc_final: 0.5542 (tpt-90) REVERT: A 135 MET cc_start: 0.7041 (ttt) cc_final: 0.6775 (ttt) REVERT: A 266 ARG cc_start: 0.7771 (tmt170) cc_final: 0.4745 (mtt180) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.1252 time to fit residues: 11.0959 Evaluate side-chains 71 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 0.0170 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.0070 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.173375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154439 restraints weight = 6599.561| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.42 r_work: 0.3587 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5835 Z= 0.106 Angle : 0.430 6.017 7938 Z= 0.231 Chirality : 0.038 0.139 936 Planarity : 0.004 0.040 962 Dihedral : 11.514 73.856 987 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.84 % Allowed : 13.42 % Favored : 85.74 % 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 aren not related in a simple way. whole: 1.48 (0.33), residues: 694 helix: 1.69 (0.25), residues: 476 sheet: -1.39 (0.77), residues: 38 loop : -0.26 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 208 TYR 0.012 0.001 TYR A 338 PHE 0.009 0.001 PHE B 224 TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5835) covalent geometry : angle 0.42975 ( 7938) hydrogen bonds : bond 0.03757 ( 336) hydrogen bonds : angle 3.95346 ( 987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.225 Fit side-chains REVERT: A 19 LYS cc_start: 0.8258 (ttpt) cc_final: 0.8004 (ptpt) REVERT: A 36 THR cc_start: 0.8229 (m) cc_final: 0.8016 (m) REVERT: A 78 ARG cc_start: 0.7551 (mmm160) cc_final: 0.5650 (tpt-90) REVERT: A 135 MET cc_start: 0.7098 (ttt) cc_final: 0.6853 (ttt) REVERT: A 266 ARG cc_start: 0.7727 (tmt170) cc_final: 0.4881 (mtt180) REVERT: B 117 HIS cc_start: 0.7320 (t70) cc_final: 0.6771 (t70) REVERT: B 139 LEU cc_start: 0.8329 (tp) cc_final: 0.8059 (tt) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.1102 time to fit residues: 10.3133 Evaluate side-chains 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148919 restraints weight = 6641.871| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.33 r_work: 0.3551 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5835 Z= 0.153 Angle : 0.470 6.014 7938 Z= 0.253 Chirality : 0.040 0.157 936 Planarity : 0.004 0.040 962 Dihedral : 11.488 74.086 987 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.84 % Allowed : 14.09 % Favored : 85.07 % 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 aren not related in a simple way. whole: 1.35 (0.33), residues: 694 helix: 1.53 (0.24), residues: 476 sheet: -0.96 (0.94), residues: 30 loop : -0.31 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 208 TYR 0.013 0.002 TYR A 59 PHE 0.013 0.001 PHE B 224 TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 5835) covalent geometry : angle 0.47010 ( 7938) hydrogen bonds : bond 0.04253 ( 336) hydrogen bonds : angle 4.08760 ( 987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.219 Fit side-chains REVERT: A 36 THR cc_start: 0.8266 (m) cc_final: 0.8044 (m) REVERT: A 78 ARG cc_start: 0.7585 (mmm160) cc_final: 0.5697 (tpt-90) REVERT: A 135 MET cc_start: 0.7030 (ttt) cc_final: 0.6811 (ttt) REVERT: A 266 ARG cc_start: 0.7800 (tmt170) cc_final: 0.4778 (mtt180) REVERT: B 117 HIS cc_start: 0.7244 (t70) cc_final: 0.6716 (t70) outliers start: 5 outliers final: 4 residues processed: 74 average time/residue: 0.1153 time to fit residues: 10.4023 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.0170 chunk 30 optimal weight: 0.7980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.172537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153567 restraints weight = 6433.350| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.42 r_work: 0.3583 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5835 Z= 0.113 Angle : 0.438 6.044 7938 Z= 0.236 Chirality : 0.038 0.144 936 Planarity : 0.004 0.039 962 Dihedral : 11.498 73.897 987 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.67 % Allowed : 14.09 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.50 (0.33), residues: 694 helix: 1.70 (0.24), residues: 476 sheet: -1.44 (0.78), residues: 38 loop : -0.23 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 208 TYR 0.012 0.001 TYR A 338 PHE 0.011 0.001 PHE B 224 TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5835) covalent geometry : angle 0.43807 ( 7938) hydrogen bonds : bond 0.03863 ( 336) hydrogen bonds : angle 3.98581 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.30 seconds wall clock time: 27 minutes 36.67 seconds (1656.67 seconds total)